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%%EOF tree-puzzle-5.2/src/0000777000076400001440000000000010075312110010170 5tree-puzzle-5.2/src/pstep.c0000644000076400001440000006723210073365074011434 /* * pstep.c * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifdef HAVE_CONFIG_H # include #endif #define EXTERN extern #include #include #include"puzzle.h" #if PARALLEL # include "ppuzzle.h" #endif /* #include"util.h" */ /* #include"pstep.h" */ int XXX=0; /* fprintf(stderr, "XXX: %d (%s:%d)\n", XXX++, __FILE__, __LINE__); */ /******************************************************************************/ /* functions for representing and building puzzling step trees */ /******************************************************************************/ /******************/ /* de-trueID-ed (HAS) */ /* writes OTU sitting on edge ed (usage: debugging) */ void writeOTU(FILE *outfp, /* output file */ int ed, /* edge to subtree */ ONEEDGE *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *column) /* current screen depth */ { /* test whether we are on a leaf */ if (edge[ed].downright == NULL && edge[ed].downleft == NULL) { *column += fputid(outfp, edge[ed].taxon); } else { /* we are NOT on a leaf */ fprintf(outfp, "("); (*column)++; /* de-trueID-ed (HAS) */ writeOTU(outfp, edge[ed].downleft->numedge, edge, edgeofleaf, nextedge, nextleaf, column); fprintf(outfp, ","); (*column)++; (*column)++; if (*column > 55) { *column = 2; fprintf(outfp, "\n "); } /* de-trueID-ed (HAS) */ writeOTU(outfp, edge[ed].downright->numedge, edge, edgeofleaf, nextedge, nextleaf, column); fprintf(outfp, ")"); (*column)++; } } /* writeOTU */ /******************/ /* de-trueID-ed (HAS) */ /* write tree (usage: debugging) */ void writetree(FILE *outfp, /* output file */ ONEEDGE *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int rootleaf) /* root leaf of tree */ { int column; column = 1; fprintf(outfp, "("); column += fputid(outfp, rootleaf) + 3; fprintf(outfp, ","); /* de-trueID-ed (HAS) */ writeOTU(outfp, edge[edgeofleaf[rootleaf]].downleft->numedge, edge, edgeofleaf, nextedge, nextleaf, &column); column++; column++; fprintf(outfp, ","); /* de-trueID-ed (HAS) */ writeOTU(outfp, edge[edgeofleaf[rootleaf]].downright->numedge, edge, edgeofleaf, nextedge, nextleaf, &column); fprintf(outfp, ");\n"); } /* writetree */ /******************/ /* checks which edge has the lowest edgeinfo if there are several edges with the same lowest edgeinfo, one of them will be selected randomly */ void minimumedgeinfo(ONEEDGE *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *minedges, int *out_howmany, int *out_minedge, /* minimum edge set */ uli *out_mininfo) /* minumum penalty */ { int i; int howmany; int minedge = 0; /* minimum edge (old search) */ uli minpenalty = 0; /* minumum penalty */ howmany = 0; for (i = 0; i < nextedge; i++) { if (howmany == 0) { /* first edge: init */ minedges[howmany++] = i; minpenalty = edge[i].edgeinfo; } else { /* -> all other edges */ if (minpenalty == edge[i].edgeinfo) { /* another min edge */ minedges[howmany++] = i; } else { /* -> not same minimum */ if (minpenalty > edge[i].edgeinfo) { /* new minimum penalty */ howmany = 1; minedges[0] = i; minpenalty = edge[i].edgeinfo; } /* if new minimum */ } /* same minimum */ } /* if all other edges */ } #if 0 if (howmany > 1) *out_minedge = minedges[randominteger(howmany)]; else *out_minedge = minedges[0]; #endif #if 0 #endif if (howmany > 1) { /* draw random edge */ int k, randomnum; randomnum = randominteger(howmany) + 1; /* 1 to howmany */ i = -1; for (k = 0; k < randomnum; k++) { do { i++; } while (edge[i].edgeinfo != minpenalty); minedge = i; } } else { minedge = minedges[0]; } *out_minedge=minedge; #if 0 #endif *out_mininfo=minpenalty; *out_howmany=howmany; } /* minimumedgeinfo */ /******************/ /* clear all edgeinfos */ void resetedgeinfo(ONEEDGE *edge, /* edge array */ int nextedge) /* next free edge idx */ { int i; for (i = 0; i < nextedge; i++) edge[i].edgeinfo = 0; } /* resetedgeinfo */ /******************/ /* initialize tree with the following starting configuration * A(=0) * [up =NULL] * [downleft =1] * [downright=2] * * | * | 0 * | * /^\ * * * * / \ * 1 / \ 2 * / \ * /| |\ * * C(=1) B(=2) * [up =0] [up =0] * [downleft =NULL] [downleft =NULL] * [downright=NULL] [downright=NULL] * * nextedge = 3 * nextleaf = 3 * */ /*******************************************************/ /* routines specific for the original O(n^5) algorithm */ /*******************************************************/ #ifdef PSTEP_ORIG /* de-trueID-ed done (HAS) */ void inittree_orig(ONEEDGE **edge, /* out: new array of edges */ int **edgeofleaf,/* out: array of external edge ptrs */ int *rootleaf, /* out: rooting leaf (=trueID[0]) */ int Maxspc, /* in: Number of species (n) */ int Maxbrnch, /* in: Number of branches (2n-3) */ int *nextedge, /* out: next free edge index (=3) */ int *nextleaf, /* out: next free leaf index (=3) */ int *trueID) { int i, j; ONEEDGE *tmpedge; int *tmpedgeofleaf; /* allocate the memory for the whole tree */ /* allocate memory for vector with all the edges of the tree */ tmpedge = (ONEEDGE *) calloc((size_t) Maxbrnch, sizeof(ONEEDGE) ); if (tmpedge == NULL) maerror("edge in inittree"); *edge = tmpedge; /* allocate memory for vetmpctor with edge numbers of leaves */ tmpedgeofleaf = (int *) calloc((size_t) Maxspc, sizeof(int) ); if (tmpedgeofleaf == NULL) maerror("edgeofleaf in inittree"); for (j = 0; j < Maxspc; j++) tmpedgeofleaf[j]=-1; *edgeofleaf = tmpedgeofleaf; /* allocate memory for all the edges the edge map */ for (i = 0; i < Maxbrnch; i++) { (tmpedge)[i].edgemap = (int *) calloc((size_t) Maxbrnch, sizeof(int) ); if (tmpedge[i].edgemap == NULL) maerror("edgemap in inittree"); for (j = 0; j < Maxspc; j++) (tmpedge)[i].edgemap[j]=-1; /* number/init all edges */ tmpedge[i].numedge = i; tmpedge[i].taxon = -1; } /* initialize tree */ *nextedge = 3; *nextleaf = 3; /* edge maps */ (tmpedge[0].edgemap)[0] = NOWHERE; /* you are on the right edge */ (tmpedge[0].edgemap)[1] = DOWNLEFT; /* go down left for 2nd taxon */ (tmpedge[0].edgemap)[2] = DOWNRIGHT; /* go down right for 3rd taxon */ (tmpedge[1].edgemap)[0] = UP; /* go up for 1st taxon */ (tmpedge[1].edgemap)[1] = NOWHERE; /* you are on the right edge */ (tmpedge[1].edgemap)[2] = UPDOWNRIGHT; /* go up/down right for 2nd taxon */ (tmpedge[2].edgemap)[0] = UP; /* go up for 1st taxon */ (tmpedge[2].edgemap)[1] = UPDOWNLEFT; /* go up/down left for 2nd taxon */ (tmpedge[2].edgemap)[2] = NOWHERE; /* you are on the right edge */ /* interconnection */ tmpedge[0].up = NULL; tmpedge[0].downleft = &tmpedge[1]; tmpedge[0].downright = &tmpedge[2]; tmpedge[1].up = &tmpedge[0]; tmpedge[1].downleft = NULL; tmpedge[1].downright = NULL; tmpedge[2].up = &tmpedge[0]; tmpedge[2].downleft = NULL; tmpedge[2].downright = NULL; /* taxon IDs of leaves */ tmpedge[0].taxon = trueID[0]; tmpedge[1].taxon = trueID[1]; tmpedge[2].taxon = trueID[2]; /* edges of leaves */ tmpedgeofleaf[trueID[0]] = 0; tmpedgeofleaf[trueID[1]] = 1; tmpedgeofleaf[trueID[2]] = 2; /* uppest edge =: root edge*/ *rootleaf = trueID[0]; } /* inittree_orig */ /******************/ /* add next leaf on the specified edge */ void addnextleaf_orig(int dockedge, /* insert here */ ONEEDGE *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int rootleaf, /* uppest leaf */ int Maxspc, /* No. of species */ int Maxbrnch, /* No. of branches */ int *in_nextedge, /* next free edge idx */ int *in_nextleaf, /* next free leaf idx */ ivector permut) /* permutation vector */ { int nextedge; int nextleaf; nextedge=*in_nextedge; nextleaf=*in_nextleaf; if (dockedge >= nextedge) { /* Trying to add leaf nextleaf to nonexisting edge dockedge */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR F TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } if (nextleaf >= Maxspc) { /* Trying to add leaf nextleaf to a tree with Maxspc leaves */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR G TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } /* necessary change in edgeofleaf if dockedge == root edge */ if (edgeofleaf[rootleaf] == dockedge) edgeofleaf[rootleaf] = nextedge; /* adding nextedge to the tree */ edge[nextedge].up = edge[dockedge].up; edge[nextedge].downleft = &edge[dockedge]; edge[nextedge].downright = &edge[nextedge+1]; edge[dockedge].up = &edge[nextedge]; /* if not root edge: connect ancestor to internal edge (nextedge) */ if (edge[nextedge].up != NULL) { if ( ((edge[nextedge].up)->downleft) == &edge[dockedge] ) (edge[nextedge].up)->downleft = &edge[nextedge]; else (edge[nextedge].up)->downright = &edge[nextedge]; } /* adding new external edge (nextedge+1) to the tree */ edge[nextedge+1].up = &edge[nextedge]; edge[nextedge+1].downleft = NULL; edge[nextedge+1].downright = NULL; edge[nextedge+1].taxon = permut[nextleaf]; edgeofleaf[permut[nextleaf]] = nextedge+1; /* update edge direction maps */ updateedgemap_orig(dockedge, edge, nextedge); nextleaf++; nextedge = nextedge + 2; *in_nextedge=nextedge; *in_nextleaf=nextleaf; } /* addnextleaf */ /******************/ /* update edgemap */ void updateedgemap_orig(int dockedge, /* insert here */ ONEEDGE *edge, /* edge array */ int nextedge) /* next free edge idx */ { int i; /* the two new edges get info about the old edges: */ /* - nextedge (internal edge) */ for (i = 0; i < nextedge; i++) { switch ( (edge[dockedge].edgemap)[i] ) { /* down right changes to down left */ case DOWNRIGHT: (edge[nextedge].edgemap)[i] = DOWNLEFT; break; /* null changes to down left */ case NOWHERE: (edge[nextedge].edgemap)[i] = DOWNLEFT; break; /* shouldn't happen */ case -1: fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR G2 TO DEVELOPERS! Unknown direction (leaf %d: %d).\n\n\n", i, (edge[dockedge].edgemap)[i]); # if PARALLEL PP_Finalize(); # endif exit(1); break; default: (edge[nextedge].edgemap)[i] = (edge[dockedge].edgemap)[i]; break; } /* switch */ } /* for i */ /* - nextedge+1 (external edge) */ for (i = 0; i < nextedge; i++) { switch ( (edge[dockedge].edgemap)[i] ) { /* up/down left changes to up */ case UPDOWNLEFT: (edge[nextedge+1].edgemap)[i] = UP; break; /* up/down right changes to up */ case UPDOWNRIGHT: (edge[nextedge+1].edgemap)[i] = UP; break; /* down left changes to up/down left */ case DOWNLEFT: (edge[nextedge+1].edgemap)[i] = UPDOWNLEFT; break; /* down right changes to up/down left */ case DOWNRIGHT: (edge[nextedge+1].edgemap)[i] = UPDOWNLEFT; break; /* null changes to up/down left */ case NOWHERE: (edge[nextedge+1].edgemap)[i] = UPDOWNLEFT; break; /* up stays up */ case UP: (edge[nextedge+1].edgemap)[i] = (edge[dockedge].edgemap)[i]; break; /* shouldn't happen */ default: fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR G1 TO DEVELOPERS! Unknown direction (leaf %d: %d).\n\n\n", i, (edge[dockedge].edgemap)[i]); # if PARALLEL PP_Finalize(); # endif exit(1); break; } /* switch */ } /* for i */ /* old internal edge (dockedge) */ for (i = 0; i < nextedge; i++) { switch ( (edge[dockedge].edgemap)[i] ) { /* up/down right changes to up */ case UPDOWNRIGHT: (edge[dockedge].edgemap)[i] = UP; break; /* up/down left changes to up */ case UPDOWNLEFT: (edge[dockedge].edgemap)[i] = UP; break; /* shouldn't happen */ case -1: fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR G3 TO DEVELOPERS! Unknown direction (leaf %d: %d).\n\n\n", i, (edge[dockedge].edgemap)[i]); # if PARALLEL PP_Finalize(); # endif exit(1); break; default: break; } /* switch */ } /* for i */ /* all edgemaps are updated for the two new edges: */ /* new internal edge (nextedge) */ (edge[nextedge].edgemap)[nextedge] = NOWHERE; /* to itself */ (edge[nextedge].edgemap)[nextedge+1] = DOWNRIGHT; /* to new ext. edge: down right */ /* new external edge (nextedge+1) */ (edge[nextedge+1].edgemap)[nextedge] = UP; /* to new int. edge: up */ (edge[nextedge+1].edgemap)[nextedge+1] = NOWHERE; /* to itself */ /* from all other edges to the new edges */ for (i = 0; i < nextedge; i++) { (edge[i].edgemap)[nextedge] = (edge[i].edgemap)[dockedge]; (edge[i].edgemap)[nextedge+1] = (edge[i].edgemap)[dockedge]; } /* an extra: from dockedge to the new edges */ (edge[dockedge].edgemap)[nextedge] = UP; /* up */ (edge[dockedge].edgemap)[nextedge+1] = UPDOWNRIGHT; /* up/down right */ } /* updateedgemap_orig */ /******************/ /* free memory (to be called after inittree) */ void freetree_orig(ONEEDGE *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc) /* No. of species */ { int i; for (i = 0; i < 2 * Maxspc - 3; i++) free(edge[i].edgemap); free(edge); free(edgeofleaf); } /* freetree */ /******************/ /* increment all edgeinfo between leaf A and B */ /* de-trueID-ed (HAS) nothing done */ void incrementedgeinfo_orig(int A, /* start leaf of penalty path */ int B, /* start leaf of penalty path */ ONEEDGE *edge, /* edge array */ int *edgeofleaf) /* ext. edge idx array */ { int curredge, finaledge, nextstep; if (A == B) return; finaledge = edgeofleaf[B]; curredge = edgeofleaf[A]; (edge[curredge].edgeinfo)++; while (curredge != finaledge) { /* nextstep = (edge[curredge].edgemap)[finaledge]; (HAS) ???*/ nextstep = (edge[curredge].edgemap)[finaledge]; switch (nextstep) { /* up */ case UP: curredge = (edge[curredge].up)->numedge; break; /* up/down left */ case UPDOWNLEFT: curredge = ((edge[curredge].up)->downleft)->numedge; break; /* up/down right */ case UPDOWNRIGHT: curredge = ((edge[curredge].up)->downright)->numedge; break; /* down left */ case DOWNLEFT: curredge = (edge[curredge].downleft)->numedge; break; /* down right */ case DOWNRIGHT: curredge = (edge[curredge].downright)->numedge; break; /* shouldn't happen */ default: fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR G4 TO DEVELOPERS! Unknown direction (leaf %d: %d).\n\n\n", finaledge, nextstep); # if PARALLEL PP_Finalize(); # endif exit(1); break; } /* switch */ (edge[curredge].edgeinfo)++; } /* while on path */ } /* incrementedgeinfo_orig */ /******************/ /* trueID-ed (HAS) */ /* perform one single puzzling step to produce one intermediate tree */ void onepstep_orig( /* PStep (intermediate) tree topol: */ ONEEDGE **edge, /* out: new array of edges */ int **edgeofleaf, /* out: array of extern edge ptrs */ int *rootleaf, /* out: root leaf in topol, starting perm[0] */ unsigned char *quartettopols, /* in: quartetblock with all topols */ int Maxspc, /* in: Number of species (n) */ ivector permut) /* in: species permutation (trueID) */ { /* local variables: */ int Maxbrnch = (2*Maxspc)-3; /* Number of branches (2n-3) */ int nextedge; /* next free edge index (=3) */ int nextleaf; /* next free leaf index (=3) */ int minedge; /* insertion edge of minimum penalty */ uli mininfo; /* minimum penalty */ int a, b, c, i; /* quartet leaves, i to be inserted */ int chooseX, chooseY; /* end leaves of penalty path */ ONEEDGE *tmpedge; /* new array of edges */ int *tmpedgeofleaf; /* array of extern edge ptrs */ int tmprootleaf; /* root edge */ int *minedges; int howmany; minedges = (int *) calloc((size_t) Maxspc, sizeof(int)); if (minedges == NULL) maerror("minimal edge set in onepstep_orig"); /* allocate and initialize new tree topology */ inittree_orig(&tmpedge, &tmpedgeofleaf, &tmprootleaf, Maxspc, Maxbrnch, &nextedge, &nextleaf, permut); /* adding all other leafs */ for (i = 3; i < Maxspc; i++) { /* clear all edgeinfos */ resetedgeinfo(tmpedge, nextedge); /* * core of quartet puzzling algorithm */ for (a = 0; a < nextleaf - 2; a++) for (b = a + 1; b < nextleaf - 1; b++) for (c = b + 1; c < nextleaf; c++) { /* check which two leaves out of a,b,c are closer related to each other than to leaf i according to a least squares fit of the continous Bayesian weights to the seven trivial "attractive regions". We assign a score of 1 to all edges on the penalty path between these two leaves chooseX and chooseY */ /* de-trueID-ed (HAS) */ checkquartet(permut[a], permut[b], permut[c], permut[i], &chooseX, &chooseY); incrementedgeinfo_orig(chooseX, chooseY, tmpedge, tmpedgeofleaf); } /* for all quartets q=(a,b,c,i) */ /* find out which edge has lowest edgeinfo */ minimumedgeinfo(tmpedge, tmpedgeofleaf, nextedge, nextleaf, minedges, &howmany, &minedge, &mininfo); /* add the next leaf on minedge */ addnextleaf_orig(minedge, tmpedge, tmpedgeofleaf, tmprootleaf, Maxspc, Maxbrnch, &nextedge, &nextleaf, permut); } /* adding all other leafs */ *edge = tmpedge; /* export tree topology */ *edgeofleaf = tmpedgeofleaf; /* export array of extern edge ptrs */ *rootleaf = tmprootleaf; /* export root edge */ free(minedges); } /* onepstep_orig */ #endif /* PSTEP_ORIG */ /**********************************************************/ /* routines specific for the split-based O(n^4) algorithm */ /**********************************************************/ #ifdef PSTEP_SPLIT # include"split.c" #endif /* PSTEP_SPLIT */ /********************************************************/ /* routines specific for the recursive O(n^4) algorithm */ /********************************************************/ #ifdef PSTEP_RECUR # include"recur.c" #endif /* PSTEP_RECUR */ /*********************************************************/ /* routines specific for the MRCA-based O(n^4) algorithm */ /* (suggested by Vincent Berry) */ /*********************************************************/ #ifdef PSTEP_MRCA # include"mrca.c" #endif /* PSTEP_MRCA */ /************************************************************************/ /* global function of the puzzling step */ /************************************************************************/ /* perform Numtrial single puzzling steps constructing Numtrial intermediate */ /* trees, sort each of them and extract splits for consensus step */ void allpstep(uli Numtrial, /* in: no. psteps to perform */ unsigned char *quartetinfo, /* in: quartetblock with all topols*/ int Maxspc, /* in: Number of species (n) */ int fixedorder_optn) /* in: 'fixed' anchored RNG (debug)*/ { /* misc variables */ ivector trueIDtmp; /* species permutation (trueID) */ uli Currtrial; /* step counter */ # ifdef PSTEP_BENCH time_t benchtime0, benchtime1; # endif /* PSTEP_BENCH */ /* PStep (intermediate) tree topol: */ ONEEDGE *tmpedgeset; /* array of edges */ int *tmpedgeofleaf; /* array of extern edge pointers */ int psteprootleaf; /* root edge */ /* for unique sorting of tree topologies */ int *ctree; /* sort tree */ int startnode; /* root in sort tree */ char *trstr; /* phylip tree string */ treelistitemtype *treeitem; /* list entry of tree */ # if PARALLEL cmatrix *bp; /* temporary buffer for splits in slaves */ uli n; /* step count for init/free split buffer */ # endif /* PARALLEL */ # if PARALLEL /* add times to arry */ addtimes(GENERAL, &tarr); /* alloc temporary split memory */ bp = (cmatrix *) calloc((size_t) Numtrial, sizeof(void *)); for(n=0; n phylip tree string */ trstr=sprintfctree(ctree, psteptreestrlen); /* add sorted tree to unique tree list */ treeitem = addtree2list(&trstr, 1, &psteptreelist, &psteptreenum, &psteptreesum); # if ! PARALLEL /* output unique tree to trace list, if option set */ /* not done on slave processes */ if((listqptrees == PSTOUT_LIST) || (listqptrees == PSTOUT_LISTORDER)) { /* print: order no/# topol per this id/tree id/sum of unique topologies/sum of trees so far */ fprintf(qptlist, "%ld.\t1\t%d\t%d\t%d\t%d\n", Currtrial + 1, (*treeitem).count, (*treeitem).id, psteptreenum, psteptreesum); } # endif /* ! PARALLEL */ # ifdef VERBOSE1 printf("%s\n", trstr); printfsortedpstrees(psteptreelist); # endif /* free sorting tree structure */ freectree(&ctree); /* free tree before building the next tree */ # ifdef PSTEP_ORIG freetree_orig(tmpedgeset, tmpedgeofleaf, Maxspc); # endif /* PSTEP_ORIG */ # ifdef PSTEP_SPLIT freetree_split(tmpedgeset, tmpedgeofleaf, Maxspc); # endif /* PSTEP_SPLIT */ # ifdef PSTEP_RECUR freetree_recur(tmpedgeset, tmpedgeofleaf, Maxspc); # endif /* PSTEP_RECUR */ # ifdef PSTEP_MRCA freetree_mrca(tmpedgeset, tmpedgeofleaf, Maxspc); # endif /* PSTEP_MRCA */ # if ! PARALLEL checktime(&time0, &time1, &time2, Currtrial, Numtrial, &mflag); # endif /* ! PARALLEL */ addtimes(PUZZLING, &tarr); } /* for Numtrials */ free_ivector(trueIDtmp); # ifdef PSTEP_BENCH time(&benchtime1); fprintf(stderr,"The %s needed: %.0fs = %fmin for %ld puzzlings on %d taxa\n", PSTEPALGNAME, (double)(benchtime1-benchtime0), (double)(benchtime1-benchtime0)/60.0, Numtrial, Maxspc); # endif /* PSTEP_BENCH */ # if PARALLEL /* in slaves: send results: splits, trees */ PP_SendSplitsBlock(Maxspc, Numtrial, bp, psteptreenum, psteptreelist); /* free temporary split memory */ for (Currtrial = 0; Currtrial < Numtrial; Currtrial++) { free_cmatrix(bp[Currtrial]); } free(bp); /* sent! Thus, in slave process not needed any more */ freetreelist(&psteptreelist, &psteptreenum, &psteptreesum); # endif /* PARALLEL */ } /* allpstep */ tree-puzzle-5.2/src/pstep.h0000644000076400001440000003541410073365115011432 /* * pstep.h * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifndef PSTEP_H #define PSTEP_H #include #include #include"puzzle.h" #include"util.h" /* #include"newpstep.h" */ /******************************************************************/ /* switch puzzling step algorithm */ /******************************************************************/ #ifndef PSTEP_RECUR # define PSTEP_RECUR #endif /* PSTEP_RECUR */ #ifdef PSTEP_SPLIT # define PSTEPALGNAME "split-based puzzling step algorithm" # ifdef PSTEP_ORIG # undef PSTEP_ORIG # endif /* PSTEP_ORIG */ # ifdef PSTEP_MRCA # undef PSTEP_MRCA # endif /* PSTEP_MRCA */ # ifdef PSTEP_RECUR # undef PSTEP_RECUR # endif /* PSTEP_RECUR */ #endif /* PSTEP_SPLIT */ #ifdef PSTEP_MRCA # define PSTEPALGNAME "mrca-based puzzling step algorithm" # ifdef PSTEP_ORIG # undef PSTEP_ORIG # endif /* PSTEP_ORIG */ # ifdef PSTEP_SPLIT # undef PSTEP_SPLIT # endif /* PSTEP_SPLIT */ # ifdef PSTEP_RECUR # undef PSTEP_RECUR # endif /* PSTEP_RECUR */ #endif /* PSTEP_MRCA */ #ifdef PSTEP_ORIG # define PSTEPALGNAME "original puzzling step algorithm" # ifdef PSTEP_MRCA # undef PSTEP_MRCA # endif /* PSTEP_MRCA */ # ifdef PSTEP_SPLIT # undef PSTEP_SPLIT # endif /* PSTEP_SPLIT */ # ifdef PSTEP_RECUR # undef PSTEP_RECUR # endif /* PSTEP_RECUR */ #endif /* PSTEP_ORIG */ #ifdef PSTEP_RECUR # define PSTEPALGNAME "recursive puzzling step algorithm" # ifdef PSTEP_ORIG # undef PSTEP_ORIG # endif /* PSTEP_ORIG */ # ifdef PSTEP_MRCA # undef PSTEP_MRCA # endif /* PSTEP_MRCA */ # ifdef PSTEP_SPLIT # undef PSTEP_SPLIT # endif /* PSTEP_SPLIT */ #endif /* PSTEP_RECUR */ /******************************************************************/ #define NOWHERE 0 #define UP 1 #define UPDOWNLEFT 2 #define UPDOWNRIGHT 3 #define DOWNLEFT 4 #define DOWNRIGHT 5 #define STARTING 6 /******************************************************************/ /* tree structure */ typedef struct oneedge { /* pointer to other three edges */ struct oneedge *up; struct oneedge *downleft; struct oneedge *downright; int numedge; /* number of edge (index) */ int taxon; /* taxon number */ uli edgeinfo; /* value of this edge (penalty) */ # ifdef PSTEP_ORIG int *edgemap; /* pointer to the local edgemap array */ # endif /* PSTEP_ORIG */ # ifdef PSTEP_SPLIT uli penalty; /* penalty of this edge */ int *split; /* cluster array (up: 0..upsize-1; */ /* down: maxspc-1..maxspc-downsize */ int upsize; /* size of root-ward cluster */ int downsize; /* size of non-root-ward cluster */ # endif /* PSTEP_SPLIT */ # ifdef PSTEP_RECUR uli penalty; /* penalty of this edge */ int *cluster; /* leaf cluster of edge (0..clsize-1; */ int clsize; /* size of non-root-ward cluster */ uli submatrsum;/* sum of all neibor-matr cluster entries */ uli allsum; /* sum of all cluster ext. edge penalty */ # endif /* PSTEP_RECUR */ # ifdef PSTEP_MRCA uli penalty; /* penalty of this edge */ uli *penaltyprop; /* penalties to propagated to the leaves */ int *cluster; /* leaf cluster of edge (0..clsize-1; */ int clsize; /* size of non-root-ward cluster */ # endif /* PSTEP_MRCA */ } ONEEDGE; /*****************************************************************************/ /* A bit of documentation: (HAS) */ /*****************************************************************************/ /* Tree initialization: * -------------------- * * A puzzling step tree is initialized like this: * * 2 * 0 +------- C(=2) * A(=0) -----+ * +------- B(=1) * 1 * * * more detailed: * * A(=0) * [up =NULL] * [downleft =ptr(1)] * [downright=ptr(2)] * PSTEP_SPLIT: * [upcluster=0] * [downcluster=1,2] * [upsize=1] * [downsize=2] * PSTEP_RECUR, PSTEP_MRCA: * [cluster=t1,t2] * [clsize=2] * * o * | * | * +-------------+--------------+ * | | * | | * o o * * C(=1) B(=2) * [up =ptr(0)] [up =ptr(0)] * [downleft =NULL] [downleft =NULL] * [downright=NULL] [downright=NULL] * PSTEP_SPLIT: * [upcluster=t0,t2] [upcluster=t0,t1] * [downcluster=t1] [downcluster=t2] * [upsize=2] [upsize=2] * [downsize=1] [downsize=1] * PSTEP_RECUR, PSTEP_MRCA: * [cluster=t1] [cluster=t2] * [clsize=1] [clsize=1] * * PSTEP_MRCA: * MRCA [t0,*] = 0 * MRCA [t1,t2] = 0 * * nextedge = 3 * nextleaf = 3 * and set according edge maps (_orig, PSTEP_ORIG), * split lists (_split, PSTEP_SPLIT), * cluster lists (_recur, PSTEP_MRCA), or * MRCA matrix (_mrca, PSTEP_MRCA), * * * * Adding leaves to works like this: * -------------------------------------------- * * * | * | nextedge * | | * | dockedge insert /^\ * | ========> * * * /^\ / \ * dockedge / \ nextedge+1 * / \ * /| |\ permut[nextleaf] * */ /*****************************************************************************/ /* internal functions for representing and building puzzling step trees */ /*****************************************************************************/ /* writes OTU sitting on edge ed (usage: debugging) */ void writeOTU(FILE *outfp, /* output file */ int ed, /* edge to subtree */ ONEEDGE *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *column); /* current screen depth */ /* write tree (usage: debugging) */ void writetree(FILE *outfp, /* output file */ ONEEDGE *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int rootleaf); /* root leaf of tree */ /* clear all edgeinfos */ void resetedgeinfo(ONEEDGE *edge, /* edge array */ int nextedge); /* next free edge idx */ /* checks which edge has the lowest edgeinfo if there are several edges with the same lowest edgeinfo, one of them will be selected randomly */ void minimumedgeinfo(ONEEDGE *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *minedges, int *out_howmany, int *out_minedge, /* minimum edge set */ uli *out_mininfo); /* minumum penalty */ /*******************************************************/ /* routines specific for the original O(n^5) algorithm */ /*******************************************************/ /* initialize tree with the following starting configuration (see above) */ void inittree_orig(ONEEDGE **edge, /* out: new array of edges */ int **edgeofleaf,/* out: array of external edge ptrs */ int *rootedge, /* out: rooting edge (=0) */ int Maxspc, /* in: Number of species (n) */ int Maxbrnch, /* in: Number of branches (2n-3) */ int *nextedge, /* out: next free edge index (=3) */ int *nextleaf, /* out: next free leaf index (=3) */ int *trueID); /* update edgemap */ void updateedgemap_orig(int dockedge, /* insert here */ ONEEDGE *edge, /* edge array */ int nextedge); /* next free edge idx */ /* add next leaf on the specified edge */ void addnextleaf_orig(int dockedge, /* insert here */ ONEEDGE *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int rootedge, /* uppest edge */ int Maxspc, /* No. of species */ int Maxbrnch, /* No. of branches */ int *in_nextedge, /* next free edge idx */ int *in_nextleaf, /* next free leaf idx */ ivector permut); /* free memory (to be called after inittree) */ void freetree_orig(ONEEDGE *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc); /* No. of species */ /* increment all edgeinfo between leaf A and B */ void incrementedgeinfo_orig(int A, /* start leaf of penalty path */ int B, /* start leaf of penalty path */ ONEEDGE *edge, /* edge array */ int *edgeofleaf); /* ext. edge idx array */ /*********/ /* perform one single puzzling step to produce one intermediate tree */ void onepstep_orig( /* PStep (intermediate) tree topol: */ ONEEDGE **edge, /* out: new array of edges */ int **edgeofleaf, /* out: array of extern edge ptrs */ int *rootleaf, /* out: root leaf in topol, starting perm[0] */ unsigned char *quartettopols, /* in: quartetblock with all topols */ int Maxspc, /* in: Number of species (n) */ ivector permut); /* in: species permutation (trueID) */ /**********************************************************/ /* routines specific for the split-based O(n^4) algorithm */ /**********************************************************/ /* initialize tree with the following starting configuration (see above) */ void inittree_split(ONEEDGE **edge, /* out: new array of edges */ int **edgeofleaf,/* out: array of external edge ptrs */ int *rootedge, /* out: rooting edge (=0) */ int Maxspc, /* in: Number of species (n) */ int Maxbrnch, /* in: Number of branches (2n-3) */ int *nextedge, /* out: next free edge index (=3) */ int *nextleaf, /* out: next free leaf index (=3) */ int *trueID); #if 0 /* update edgemap */ void updateedgemap_split(int dockedge, /* insert here */ ONEEDGE *edge, /* edge array */ int nextedge); /* next free edge idx */ #endif /* add next leaf on the specified edge */ void addnextleaf_split(int dockedge, /* insert here */ ONEEDGE *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int rootedge, /* uppest edge */ int Maxspc, /* No. of species */ int Maxbrnch, /* No. of branches */ int *in_nextedge, /* next free edge idx */ int *in_nextleaf, /* next free leaf idx */ ivector permut); /* free memory (to be called after inittree) */ void freetree_split(ONEEDGE *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc); /* No. of species */ #if 0 /* increment all edgeinfo between leaf A and B */ void incrementedgeinfo_split(int A, /* start leaf of penalty path */ int B, /* start leaf of penalty path */ ONEEDGE *edge, /* edge array */ int *edgeofleaf); /* ext. edge idx array */ #endif /*********/ /* perform one single puzzling step to produce one intermediate tree */ void onepstep_split( /* PStep (intermediate) tree topol: */ ONEEDGE **edge, /* out: new array of edges */ int **edgeofleaf, /* out: array of extern edge ptrs */ int *rootleaf, /* out: root leaf in topol, starting perm[0] */ unsigned char *quartettopols, /* in: quartetblock with all topols */ int Maxspc, /* in: Number of species (n) */ ivector permut); /* in: species permutation (trueID) */ /*****************************************************************************/ /* global functions for representing and building puzzling step trees */ /*****************************************************************************/ /* perform Numtrial single puzzling steps constructing Numtrial intermediate */ /* trees, sort each of them and extract splits for consensus step */ void allpstep(uli Numtrial, /* in: no. psteps to perform */ unsigned char *quartetinfo, /* in: quartetblock with all topols*/ int Maxspc, /* in: Number of species (n) */ int fixedorder_optn); /* in: 'fixed' anchored RNG (debug)*/ #endif /* PSTEP_H */ tree-puzzle-5.2/src/ml.h0000644000076400001440000003603610073365127010713 /* * ml.h * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifndef _ML_ #define _ML_ /* values for mlmode */ #define ML_QUART 1 #define ML_TREE 2 #define NJ_TREE 3 #if 0 /* values for rhettype */ #define MLUNIFORMRATE 0 #define MLGAMMARATE 1 #define MLTWORATE 2 #define MLMIXEDRATE 3 #endif /* values for rhetmode */ #define UNIFORMRATE 0 #define GAMMARATE 1 #define TWORATE 2 #define MIXEDRATE 3 /* definitions */ #define MINTS 0.20 /* Ts/Tv parameter */ #define MAXTS 30.0 #define MINYR 0.10 /* Y/R Ts parameter */ #define MAXYR 6.00 #define MINFI 0.00 /* fraction invariable sites */ #define MAXFI 0.99 /* only for input */ #define MINGE 0.01 /* rate heterogeneity parameter */ #define MAXGE 0.99 #define MINCAT 4 /* discrete Gamma categories */ #define MAXCAT 16 #define RMHROOT 5.0 /* upper relative bound for height of root */ #define MAXARC 900.0 /* upper limit on branch length (PAM) = 6.0 */ #define MINARC 0.001 /* lower limit on branch length (PAM) = 0.00001 */ #ifdef USE_ADJUSTABLE_EPS /* error in branch length (PAM) = 0.000001 */ # define EPSILON_BRANCH_DEFAULT 0.0001 # define EPSILON_BRANCH epsilon_branch EXTERN double epsilon_branch; #else # define EPSILON_BRANCH 0.0001 #endif #ifdef USE_ADJUSTABLE_EPS /* error in node and root heights */ # define EPSILON_HEIGHTS_DEFAULT 0.0001 # define EPSILON_HEIGHTS epsilon_heights EXTERN double epsilon_heights; #else # define EPSILON_HEIGHTS 0.0001 #endif #ifdef USE_ADJUSTABLE_EPS # if (EXTERN != extern) double epsilon_branch = EPSILON_BRANCH_DEFAULT; double epsilon_heights = EPSILON_HEIGHTS_DEFAULT; # endif #endif #define MAXIT 100 /* maximum number of iterates of smoothing */ #define MINFDIFF 0.00002 /* lower limit on base frequency differences */ #define MINFREQ 0.0001 /* lower limit on base frequencies = 0.01% */ #define NUMQBRNCH 5 /* number of branches in a quartet */ #define NUMQIBRNCH 1 /* number of internal branches in a quartet */ #define NUMQSPC 4 /* number of sequences in a quartet */ /* 2D minimisation */ #ifdef USE_ADJUSTABLE_EPS /* epsilon substitution process estimation */ # define EPSILON_SUBSTPARAM_DEFAULT 0.01 # define EPSILON_SUBSTPARAM epsilon_substparam EXTERN double epsilon_substparam; #else # define EPSILON_SUBSTPARAM 0.01 #endif #ifdef USE_ADJUSTABLE_EPS /* epsilon rate heterogeneity estimation */ # define EPSILON_RATEPARAM_DEFAULT 0.01 # define EPSILON_RATEPARAM epsilon_rateparam EXTERN double epsilon_rateparam; #else # define EPSILON_RATEPARAM 0.01 #endif #ifdef USE_ADJUSTABLE_EPS # if (EXTERN != extern) double epsilon_substparam = EPSILON_SUBSTPARAM_DEFAULT; double epsilon_rateparam = EPSILON_RATEPARAM_DEFAULT; # endif #endif /* quartet series */ #define MINPERTAXUM 2 #define MAXPERTAXUM 6 #define TSDIFF 0.20 #define YRDIFF 0.10 /* type definitions */ typedef struct node { struct node *isop; /* pointers within node (nodes) */ struct node *kinp; /* pointers between nodes (branches) */ int descen; int number; double length; /* branch length inferred (no clock) */ double lengthc; /* branch length inferred (clock) */ double lengthext; /* external length from usertree */ int lengthset; /* length set by usertree */ double varlen; double height; double varheight; ivector paths; /* path directions for Korbi's p-step */ cvector eprob; dcube partials; /* partial likelihoods */ char *label; /* internal labels */ } Node; typedef struct tree { Node *rootp; Node **ebrnchp; /* list of pointers to external branches */ Node **ibrnchp; /* list of pointers to internal branches */ double lklhd; /* total log-likelihood */ double lklhdc; /* total log-likelihood clock */ dmatrix condlkl; /* lhs for each pattern and non-zero rate */ double rssleast; } Tree; /* global variables */ EXTERN Node *chep; /* pointer to current height node */ EXTERN Node *rootbr; /* pointer to root branch */ EXTERN Node **heights; /* pointer to height nodes in unrooted tree */ EXTERN int Numhts; /* number of height nodes in unrooted tree */ EXTERN double hroot; /* height of root */ EXTERN double varhroot; /* variance of height of root */ EXTERN double maxhroot; /* maximal height of root */ EXTERN int locroot; /* location of root */ EXTERN int numbestroot; /* number of best locations for root */ EXTERN int clockmode; /* clocklike vs. nonclocklike computation */ EXTERN cmatrix Identif; /* sequence names */ EXTERN cmatrix Namestr; /* sequence names (delimited by '\0') */ EXTERN cmatrix Seqchar; /* ML sequence data */ EXTERN cmatrix Seqpat; /* ordered site patterns */ EXTERN ivector constpat; /* indicates constant site patterns */ EXTERN cvector seqchi; EXTERN cvector seqchj; EXTERN dcube partiali; EXTERN dcube partialj; EXTERN dcube ltprobr; /* transition probabilites (for all non-zero rates*/ EXTERN dmatrix Distanmat; /* matrix with maximum likelihood distances */ EXTERN dmatrix Evec; /* Eigenvectors */ EXTERN dmatrix Ievc; /* Inverse eigenvectors */ EXTERN double TSparam; /* Ts/Tv parameter */ EXTERN double GTR_ACrate; /* A <-> G mutation rate for GTR */ EXTERN double GTR_AGrate; /* A <-> C mutation rate for GTR */ EXTERN double GTR_ATrate; /* A <-> T mutation rate for GTR */ EXTERN double GTR_CGrate; /* C <-> G mutation rate for GTR */ EXTERN double GTR_CTrate; /* C <-> T mutation rate for GTR */ EXTERN double GTR_GTrate; /* G <-> T mutation rate for GTR */ EXTERN double tsmean, yrmean; EXTERN double YRparam; /* Y/R Ts parameter */ EXTERN double geerr; /* estimated error of rate heterogeneity */ EXTERN double Geta; /* rate heterogeneity parameter */ EXTERN double fracconst; /* fraction of constant sites */ EXTERN double fracconstpat;/* fraction of constant patterns */ EXTERN double Proportion; /* for tree drawing */ EXTERN double tserr; /* estimated error of TSparam */ EXTERN double yrerr; /* estimated error of YRparam */ EXTERN double fracinv; /* fraction of invariable sites */ EXTERN double fierr; /* estimated error of fracinv */ EXTERN dvector Brnlength; EXTERN dvector Distanvec; EXTERN dvector Eval; /* Eigenvalues of 1 PAM rate matrix */ EXTERN dvector Freqtpm; /* base frequencies */ EXTERN dvector Rates; /* rate of each of the categories */ EXTERN dmatrix iexp; EXTERN imatrix Basecomp; /* base composition of each taxon */ EXTERN ivector usedtaxa; /* list needed in the input treefile procedure */ EXTERN int numtc; /* auxiliary variable for printing rooted tree */ EXTERN int qcalg_optn; /* use quartet subsampling algorithm */ EXTERN int approxp_optn;/* approximate parameter estimation */ EXTERN int chi2fail; /* flag for chi2 test */ EXTERN int Converg; /* flag for ML convergence (no clock) */ EXTERN int Convergc; /* flag for ML convergence (clock) */ EXTERN int data_optn; /* type of sequence input data */ EXTERN int Dayhf_optn; /* Dayhoff model */ EXTERN int HKY_optn; /* use HKY model */ EXTERN int Jtt_optn; /* JTT model */ EXTERN int print_GTR_optn; /* print (restricted) GTR matrix */ EXTERN int GTR_optn; /* GTR model */ EXTERN int blosum62_optn; /* BLOSUM 62 model */ EXTERN int mtrev_optn; /* mtREV model */ EXTERN int cprev_optn; /* cpREV model */ EXTERN int vtmv_optn; /* VT model */ EXTERN int wag_optn; /* WAG model */ EXTERN int Maxsite; /* number of ML characters per taxum */ EXTERN int Maxspc; /* number of sequences */ EXTERN int mlmode; /* quartet ML or user defined tree ML */ EXTERN int nuc_optn; /* nucleotide (4x4) models */ EXTERN int Numbrnch; /* number of branches of current tree */ EXTERN int numcats; /* number of rate categories */ EXTERN int Numconst; /* number of constant sites */ EXTERN int Numconstpat; /* number of constant patterns */ EXTERN int Numibrnch; /* number of internal branches of current tree */ EXTERN int Numitc; /* number of ML iterations assumning clock */ EXTERN int Numit; /* number of ML iterations if convergence */ EXTERN int Numptrn; /* number of site patterns */ EXTERN int Numspc; /* number of sequences of current tree */ EXTERN int optim_optn; /* optimize model parameters */ EXTERN int grate_optim; /* optimize Gamma rate heterogeneity parameter */ EXTERN int SH_optn; /* SH nucleotide (16x16) model */ EXTERN int TN_optn; /* use TN model */ EXTERN int tpmradix; /* number of different states */ EXTERN int fracinv_optim; /* optimize fraction of invariable sites */ EXTERN int typ_optn; /* type of PUZZLE analysis */ EXTERN ivector Weight; /* weight of each site pattern */ EXTERN Tree *Ctree; /* pointer to current tree */ EXTERN int qca, qcb, qcc, qcd; /* quartet currently optimized */ EXTERN ivector Alias; /* link site -> corresponding site pattern */ EXTERN ivector bestrate; /* optimal assignment of rates to sequence sites*/ EXTERN int bestratefound; /* best rate per site already reconstructed ? */ /* function prototypes of all ml function */ void convfreq(dvector); void tp_radixsort(cmatrix, ivector, int, int, int *); void condenceseq(cmatrix, ivector, cmatrix, ivector, int, int, int); void countconstantsites(cmatrix, ivector, int, int, int *, int*); void evaluateseqs(void); void elmhes(dmatrix, ivector, int); void eltran(dmatrix, dmatrix, ivector, int); void mcdiv(double, double, double, double, double *, double *); void hqr2(int, int, int, dmatrix, dmatrix, dvector, dvector); void onepamratematrix(dmatrix); void eigensystem(dvector, dmatrix); void luinverse(dmatrix, dmatrix, int); void checkevector(dmatrix, dmatrix, int); void tranprobmat(void); void tprobmtrx(double, dmatrix); double comptotloglkl(dmatrix); void allsitelkl(dmatrix, dvector); void writesitelklmatrixphy(FILE *outf, int numut, int numsite, dmatrix allslkl, dmatrix allslklc, int clock); void writesitelklvectorphy(FILE *outf, char *name, int numsite, dvector aslkl); /* void writesitelklbin(FILE *, dvector); */ /* TODO */ double pairlkl(double); double mldistance(int, int, double); /*epe*/ /* double mldistance(int, int); */ void initdistan(void); void computedistan(void); void productpartials(Node *); void partialsinternal(Node *); void partialsexternal(Node *); void initpartials(Tree *); double intlkl(double); void optinternalbranch(Node *); double extlkl(double); void optexternalbranch(Node *); void finishlkl(Node *); double optlkl(Tree *); double treelkl(Tree *); void luequation(dmatrix, dvector, int); void lslength(Tree *, dvector, int, int, dvector); #if PARALLEL void lslength_par(Tree *, dvector, int, int, dvector); #endif void setextlength(Tree *, int, int, dvector); void getusertree(FILE *, cvector, int, int); Node *internalnode(Tree *, char **, int *); void constructtree(Tree *, cvector, int); void removebasalbif(cvector); void makeusertree(FILE *, int); Tree *new_tree(int, int, cmatrix); Tree *new_quartet(int, cmatrix); void free_tree(Tree *, int); void make_quartet(int, int, int, int); void changedistan(dmatrix, dvector, int); double quartet_lklhd(int, int, int, int); double quartet_alklhd(int, int, int, int); void readusertree(FILE *, int); double usertree_lklhd(int, int); double usertree_alklhd(int, int); void mlstart(void); void distupdate(int, int, int, int); void mlfinish(void); void prbranch(Node *, int, int, int, ivector, ivector, FILE *); void getproportion(double *, dvector, int); void prtopology(FILE *); void fputphylogeny(FILE *); void resulttree(FILE *outfp, int usebranch); void njtree(FILE *); void njdistantree(Tree *); void findbestratecombination(void); void printbestratecombination(FILE *); void printbestratecombinationtofile(FILE *, int); int checkedge(int); void fputsubstree(FILE *, Node *); void fputrooted(FILE *, int); void findheights(Node *); void initclock(int); double clock_alklhd(int); double heightlkl(double); void optheight(void); double rheightlkl(double); void optrheight(void); double clock_lklhd(int); int findrootedge(void); void resultheights(FILE *); /* mlparam.c */ double homogentest(int); void YangDiscreteGamma(double, int, double *); void updaterates(void); void computestat(double *, int, double *, double *); double quartetml(int, int, int, int); double opttsq(double); double optyrq(double); void optimseqevolparamsquart(void); double opttst(double); double optyrt(double); void optimseqevolparamstree(void); double optfi(double); double optge(double); void optimrateparams(void); void estimateparametersnotree(void); /* moved from puzzle1.c */ void estimateparameterstree(void); /* moved from puzzle1.c */ /* mlparam.c end */ int gettpmradix(void); void rtfdata(dmatrix, double *); int code2int(cvector, int *, int *); char *int2code(int); void jttdata(dmatrix, double *); void dyhfdata(dmatrix, double *); void mtrevdata(dmatrix, double *); void cprev45data(dmatrix, double *); void blosum62data(dmatrix, double *); void vtmvdata(dmatrix, double *); void wagdata(dmatrix, double *); #endif tree-puzzle-5.2/src/consensus.c0000644000076400001440000007641310073365134012317 /* * consensus.c * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #define EXTERN extern #include "consensus.h" #ifdef PARALLEL # include "ppuzzle.h" #endif int ZZZ=0; /* fprintf(stderr, "ZZZ: %d (%s:%d)\n", ZZZ++, __FILE__, __LINE__); */ /******************************************************************************/ /* functions for computing the consensus tree */ /******************************************************************************/ /* prepare for consensus tree analysis */ void initconsensus() { # if ! PARALLEL biparts = new_cmatrix(Maxspc-3, Maxspc); # endif /* PARALLEL */ if (Maxspc % 32 == 0) splitlength = Maxspc/32; else splitlength = (Maxspc + 32 - (Maxspc % 32))/32; numbiparts = 0; /* no pattern stored so far */ maxbiparts = 0; /* no memory reserved so far */ splitfreqs = NULL; splitpatterns = NULL; splitsizes = NULL; splitcomptemp = (uli *) calloc((size_t) splitlength, sizeof(uli) ); if (splitcomptemp == NULL) maerror("splitcomptemp in initconsensus"); } /* initconsensus */ /******************/ /* de-trueID-ed (HAS) */ /* recursive function to get bipartitions */ /* traversal should be optimazable (HAS) */ void makepart(int i, /* */ int curribrnch, /* in: current branch in traversal */ ONEEDGE *edge, /* in: tree topology */ int *edgeofleaf, /* in: ext. edge list */ cmatrix biparts, /* out: split strings, edge by edge */ int Maxspc) /* in: number of species in tree */ { if ( edge[i].downright == NULL || edge[i].downleft == NULL) { biparts[curribrnch][edge[i].taxon] = '*'; return; } else { /* still on inner branch */ makepart(edge[i].downleft->numedge, curribrnch, edge, edgeofleaf, biparts, Maxspc); makepart(edge[i].downright->numedge, curribrnch, edge, edgeofleaf, biparts, Maxspc); } } /* makepart */ /******************/ /* de-trueID-ed (HAS) */ /* compute bipartitions of current puzzling step tree */ /* traversal should be optimazable (HAS) */ void computebiparts(ONEEDGE *edge, /* in: tree topology */ int *edgeofleaf, /* in: ext. edge list */ int psteprootleaf, /* virtual root from pstep */ cmatrix biparts, /* out: splits */ int outgroup, /* in: outgroup of tree */ int Maxspc) /* in: number of taxa in tree */ { int i, j, curribrnch; curribrnch = -1; for (i = 0; i < Maxspc - 3; i++) for (j = 0; j < Maxspc; j++) biparts[i][j] = '.'; for (i = 0; i < Maxbrnch; i++) { /* (HAS) */ if (!(edgeofleaf[psteprootleaf] == i || edge[i].downright == NULL || edge[i].downleft == NULL) ) { /* check only inner branches */ curribrnch++; makepart(i, curribrnch, edge, edgeofleaf, biparts, Maxspc); /* make sure that the root is always a '*' */ if (biparts[curribrnch][outgroup] == '.') { for (j = 0; j < Maxspc; j++) { if (biparts[curribrnch][j] == '.') biparts[curribrnch][j] = '*'; else biparts[curribrnch][j] = '.'; } } } } } /* computebiparts */ /******************/ /* print out the bipartition n of all different splitpatterns */ void fprintfsplit(FILE *fp, /* outputfile stream */ uli n, /* split number */ uli *splitpatterns, /* splits */ int splitlength, /* number of ulis per split */ int Maxspc) /* number of taxa */ { int i, j; /* counter variables */ int col; /* current output column */ uli z; /* temporary variable for bit shifting */ col = 0; for (i = 0; i < splitlength; i++) { z = splitpatterns[n*splitlength + i]; for (j = 0; j < 32 && col < Maxspc; j++) { if (col % 10 == 0 && col != 0) fprintf(fp, " "); if (z & 1) fprintf(fp, "."); else fprintf(fp, "*"); z = (z >> 1); col++; } } } /* printsplit */ /******************/ /* general remarks: - every entry in consbiparts is one node of the consensus tree - for each node one has to know which taxa and which other nodes are *directly* descending from it - for every taxon/node number there is a flag that shows whether it descends from the node or not - '0' means that neither a taxon nor another node with the corresponding number decends from the node '1' means that the corresponding taxon descends from the node '2' means that the corresponding node descends from the node '3' means that the corresponding taxon and node descends from the node */ /* make new entries for new different bipartitions and count frequencies */ /* internal use: splitcomptemp */ void makenewsplitentries(cmatrix bip, /* in: split string vector */ int numspl, /* in: no. of new splits */ uli **in_splitpatterns,/* io: known compr splits */ int **in_splitsizes, /* io: kn. split sizes: '.'*/ uli **in_splitfreqs, /* io: kn. split frequences*/ uli *in_numbiparts, /* io: no. of splits so far*/ uli *in_maxbiparts, /* io: reserved memory */ int Maxspc) /* in: no. of species */ { int i, j; /* count variables */ int bpc; /* split count */ int identical; /* split identical flag */ int idflag; /* split size identical flag */ int bpsize; /* split size: count the '.' */ uli nextentry; /* temp vaiable for split amount numbiparts */ uli obpc; /* split count - old splits */ uli *splitpatternstmp; /* temp pointer, saves derefs. */ int *splitsizestmp; /* temp pointer, saves derefs. */ uli *splitfreqstmp; /* temp pointer, saves derefs. */ uli maxbipartstmp; /* split memory reserved so far */ splitpatternstmp = *in_splitpatterns; splitsizestmp = *in_splitsizes; splitfreqstmp = *in_splitfreqs; maxbipartstmp = *in_maxbiparts; /* where the next entry would be in splitpatterns */ nextentry = *in_numbiparts; for (bpc = 0; bpc < numspl; bpc++) { /* for every new bipartition */ /* convert bipartition into a more compact format */ bpsize = 0; for (i = 0; i < splitlength; i++) { splitcomptemp[i] = 0; for (j = 0; j < 32; j++) { splitcomptemp[i] = splitcomptemp[i] >> 1; if (i*32 + j < Maxspc) if (bip[bpc][i*32 + j] == '.') { /* set highest bit */ splitcomptemp[i] = (splitcomptemp[i] | 2147483648UL); bpsize++; /* count the '.' */ } } } /* compare to the *old* patterns */ identical = FALSE; for (obpc = 0; (obpc < *in_numbiparts) && (!identical); obpc++) { /* compare first partition size */ if (splitsizestmp[obpc] == bpsize) idflag = TRUE; else idflag = FALSE; /* if size is identical compare whole partition */ for (i = 0; (i < splitlength) && idflag; i++) if (splitcomptemp[i] != splitpatternstmp[obpc*splitlength + i]) idflag = FALSE; if (idflag) identical = TRUE; } if (identical) { /* if identical increase frequency */ splitfreqstmp[2*(obpc-1)]++; } else { /* create new entry */ if (nextentry == maxbipartstmp) { /* reserve more memory */ maxbipartstmp = maxbipartstmp + 2*Maxspc; splitfreqstmp = (uli *) myrealloc(splitfreqstmp, 2*maxbipartstmp * sizeof(uli) ); /* 2x: splitfreqstmp contains also an index (sorting!) */ if (splitfreqstmp == NULL) maerror("splitfreqstmp in makenewsplitentries"); splitpatternstmp = (uli *) myrealloc(splitpatternstmp, splitlength*maxbipartstmp * sizeof(uli) ); if (splitpatternstmp == NULL) maerror("splitpatternstmp in makenewsplitentries"); splitsizestmp = (int *) myrealloc(splitsizestmp, maxbipartstmp * sizeof(int) ); if (splitsizestmp == NULL) maerror("splitsizestmp in makenewsplitentries"); } splitfreqstmp[2*nextentry] = 1; /* frequency */ splitfreqstmp[2*nextentry+1] = nextentry; /* index for sorting */ for (i = 0; i < splitlength; i++) splitpatternstmp[nextentry*splitlength + i] = splitcomptemp[i]; splitsizestmp[nextentry] = bpsize; nextentry++; } } /* export new values */ *in_numbiparts = nextentry; *in_splitpatterns = splitpatternstmp; *in_splitsizes = splitsizestmp; *in_splitfreqs = splitfreqstmp; *in_maxbiparts = maxbipartstmp; } /* makenewsplitentries - new */ /***************************************************************************/ /* copy bipartition n of all different splitpatterns to consbiparts[k] */ void copysplit(uli n, uli *splitpatterns, int k, cmatrix consbipartsvec) { int i, j, col; uli z; col = 0; for (i = 0; i < splitlength; i++) { z = splitpatterns[n*splitlength + i]; for (j = 0; j < 32 && col < Maxspc; j++) { if (z & 1) consbipartsvec[k][col] = '1'; else consbipartsvec[k][col] = '0'; z = (z >> 1); col++; consbipartsvec[k][Maxspc] = '\0'; } } } /* copysplit */ /******************/ /* and the quartet topologies from the ML step. Values are */ /* stored in */ /* missing parameter: quartetinfo */ void quartsupport(int splitnum, cmatrix consbipartsvec, qsupportarr_t *qsupparr) { int n; int *clusterA; int *clusterB; int clustA = 0; int clustB = 0; int a1, a2, b1, b2; int aa1, aa2, bb1, bb2; uli fullres_pro = 0; uli fullres_con = 0; uli partres_pro = 0; uli partres_con = 0; uli unres = 0; uli missing = 0; uli qsum = 0; cvector splitstr; unsigned char tmpweight; clusterA = calloc((size_t) Maxspc, (sizeof(int))); if (clusterA == NULL) maerror("clusterA in quartsupport"); clusterB = calloc((size_t) Maxspc, (sizeof(int))); if (clusterA == NULL) maerror("clusterB in quartsupport"); splitstr = consbipartsvec[splitnum]; for(n=0; n maxnumtrees) consincluded = i + 1; } /* collect all info about majority rule consensus tree */ /* the +1 is due to the edge with the root */ /* consincluded changed to (Maxspc-3) to collect sub-50%-splits */ /* a maximum of (Maxspc-3) is possible in a Maxspc-tree (HAS) */ consconfid = new_ivector( (Maxspc-3) + 1); conssizes = new_ivector(2*(Maxspc-3) + 2); consbiparts = new_cmatrix( (Maxspc-3) + 1, Maxspc + 1); /* old routine (HAS) consconfid = new_ivector(consincluded + 1); conssizes = new_ivector(2*consincluded + 2); consbiparts = new_cmatrix(consincluded + 1, Maxspc); */ for (i = 0; i < consincluded; i++) { /* copy partition to consbiparts */ copysplit(splitfreqs[2*i+1], splitpatterns, i, consbiparts); /* frequency in percent (rounded to integer) */ consconfid[i] = (int) floor(100.0*splitfreqs[2*i]/maxnumtrees + 0.5); /* size of partition */ conssizes[2*i] = splitsizes[splitfreqs[2*i+1]]; conssizes[2*i+1] = i; } consfifty = consincluded; done = FALSE; i = consincluded; /* until maximum splits (Maxspc-3) incorporated or */ /* first incongruence found */ while ((i < (Maxspc-3)) && !done) { /* copy partition to consbiparts */ copysplit(splitfreqs[2*i+1], splitpatterns, i, consbiparts); for (scount = 0; (scount 0) && (count10 > 0) && (count00 > 0) && (count11 > 0)) done = TRUE; } } if (!done) { /* frequency in percent (rounded to integer) */ consconfid[i] = (int) floor(100.0*splitfreqs[2*i]/maxnumtrees+ 0.5); /* size of partition */ conssizes[2*i] = splitsizes[splitfreqs[2*i+1]]; conssizes[2*i+1] = i; i++; } } /* last split has same percentage as the first unincorporated, remove */ if (((uli)(i + 1) < numbiparts) && (splitfreqs[2*i] == splitfreqs[2*(i+1)])) done = TRUE; /* remove all splits with same percentage as first incongruence */ if (done) { while ((i > 0) && (splitfreqs[2*i] == splitfreqs[2*(i-1)])) i--; } if (conssub50_optn) { consincluded = i; conscongruent = i; } else { conscongruent = i; } for (i = 0; i < Maxspc; i++) consbiparts[consincluded][i] = '1'; consbiparts[consincluded][outgroup] = '0'; consconfid[consincluded] = 100; conssizes[2*consincluded] = Maxspc - 1; conssizes[2*consincluded + 1] = consincluded; /* sort bipartitions according to cluster size */ qsort(conssizes, consincluded + 1, 2*sizeof(int), intcmp); qsupportarr = malloc((size_t) (sizeof(qsupportarr_t) * consincluded)); if (qsupp_optn) { for (i = 0; i < consincluded; i++) { quartsupport(i, consbiparts, qsupportarr); } } /******************************/ /* reconstruct consensus tree */ /******************************/ for (i = 0; i < consincluded; i++) { /* try every node */ size = conssizes[2*i]; /* size of current node */ for (j = i + 1; j < consincluded + 1; j++) { /* compare only with nodes with more descendants */ if (size == conssizes[2*j]) continue; /* check whether node i is a subnode of j */ subnode = FALSE; for (k = 0; k < Maxspc && !subnode; k++) { chari = consbiparts[ conssizes[2*i+1] ][k]; if (chari != '0') { charj = consbiparts[ conssizes[2*j+1] ][k]; if (chari == charj || charj == '3') subnode = TRUE; } } /* if i is a subnode of j change j accordingly */ if (subnode) { /* remove subnode i from j */ for (k = 0; k < Maxspc; k++) { chari = consbiparts[ conssizes[2*i+1] ][k]; if (chari != '0') { charj = consbiparts[ conssizes[2*j+1] ][k]; if (chari == charj) consbiparts[ conssizes[2*j+1] ][k] = '0'; else if (charj == '3') { if (chari == '1') consbiparts[ conssizes[2*j+1] ][k] = '2'; else if (chari == '2') consbiparts[ conssizes[2*j+1] ][k] = '1'; else { /* Consensus tree [1] */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR H TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } } else { /* Consensus tree [2] */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR I TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } } } /* add link to subnode i in node j */ charj = consbiparts[ conssizes[2*j+1] ][ conssizes[2*i+1] ]; if (charj == '0') consbiparts[ conssizes[2*j+1] ][ conssizes[2*i+1] ] = '2'; else if (charj == '1') consbiparts[ conssizes[2*j+1] ][ conssizes[2*i+1] ] = '3'; else { /* Consensus tree [3] */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR J TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } } } } } /* makeconsensus */ /******************/ /* prototype for recursion */ void writenode(FILE *treefile, /* in: output stream */ int node, /* current node */ int qsupp_optn, /* 'print quartet support' flag */ qsupportarr_t *qsupparr, /* quartet support values */ int *column); /* current line position */ /* write node (writeconsensustree) */ /* missing: column */ void writenode(FILE *treefile, /* in: output stream */ int node, /* current node */ int qsupp_optn, /* 'print quartet support' flag */ qsupportarr_t *qsupparr, /* quartet support values */ int *column) /* current line position */ { int i, first; fprintf(treefile, "("); (*column)++; /* write descending nodes */ first = TRUE; for (i = 0; i < Maxspc; i++) { if (consbiparts[node][i] == '2' || consbiparts[node][i] == '3') { if (first) first = FALSE; else { fprintf(treefile, ","); (*column)++; } if ((*column) > 60) { (*column) = 2; fprintf(treefile, "\n"); } /* write node i */ writenode(treefile, i, qsupp_optn, qsupparr, column); if (qsupp_optn) { /* reliability value as internal label */ fprintf(treefile, "%d", consconfid[i]); (*column) += 3; #if 0 fprintf(treefile, "\"bs=%d|", consconfid[i]); (*column) += 7; fprintf(treefile, "f+=%.0f|", (100.0*qsupparr[i].fullres_pro/qsupparr[i].qsum)); (*column) += 7; fprintf(treefile, "p+=%.0f|", (100.0*qsupparr[i].partres_pro/qsupparr[i].qsum)); (*column) += 7; fprintf(treefile, "f-=%.0f|", (100.0*qsupparr[i].fullres_con/qsupparr[i].qsum)); (*column) += 7; fprintf(treefile, "p-=%.0f|", (100.0*qsupparr[i].partres_con/qsupparr[i].qsum)); (*column) += 7; fprintf(treefile, "ur=%.0f", (100.0*qsupparr[i].unres/qsupparr[i].qsum)); (*column) += 6; if (qsupparr[i].missing > 0) { fprintf(treefile, "|md=%.0f", (100.0*qsupparr[i].missing/qsupparr[i].qsum)); (*column) += 7; } fprintf(treefile, "/%ld\"", qsupparr[i].qsum); (*column) += 5; #endif } else { /* reliability value as internal label */ fprintf(treefile, "%d", consconfid[i]); (*column) += 3; } } } /* write descending taxa */ for (i = 0; i < Maxspc; i++) { if (consbiparts[node][i] == '1' || consbiparts[node][i] == '3') { if (first) first = FALSE; else { fprintf(treefile, ","); (*column)++; } if ((*column) > 60) { (*column) = 2; fprintf(treefile, "\n"); } (*column) += fputid(treefile, i); } } fprintf(treefile, ")"); (*column)++; } /* writenode */ /******************/ /* write consensus tree */ /* missing: consbiparts, consincluded, consconfid, */ void writeconsensustree(FILE *treefile, /* in: output stream */ int qsupp_optn, /* 'print quartsupp' flag */ qsupportarr_t *qsupparr) /* quartet support values */ { int i, first; int column; column = 1; fprintf(treefile, "("); column += fputid(treefile, outgroup) + 2; fprintf(treefile, ","); /* write descending nodes */ first = TRUE; for (i = 0; i < Maxspc; i++) { if (consbiparts[consincluded][i] == '2' || consbiparts[consincluded][i] == '3') { if (first) first = FALSE; else { fprintf(treefile, ","); /* first (outgroup) has ',' already */ column++; } if (column > 60) { column = 2; fprintf(treefile, "\n"); } /* write node i */ writenode(treefile, i, qsupp_optn, qsupparr, &column); if (qsupp_optn) { /* reliability value as internal label */ fprintf(treefile, "%d", consconfid[i]); column += 3; #if 0 fprintf(treefile, "\"bs=%d|", consconfid[i]); column += 7; fprintf(treefile, "f+=%.0f|", (100.0*qsupparr[i].fullres_pro/qsupparr[i].qsum)); column += 7; fprintf(treefile, "p+=%.0f|", (100.0*qsupparr[i].partres_pro/qsupparr[i].qsum)); column += 7; fprintf(treefile, "f-=%.0f|", (100.0*qsupparr[i].fullres_con/qsupparr[i].qsum)); column += 7; fprintf(treefile, "p-=%.0f|", (100.0*qsupparr[i].partres_con/qsupparr[i].qsum)); column += 7; fprintf(treefile, "ur=%.0f", (100.0*qsupparr[i].unres/qsupparr[i].qsum)); column += 6; if (qsupparr[i].missing > 0) { fprintf(treefile, "|md=%.0f", (100.0*qsupparr[i].missing/qsupparr[i].qsum)); column += 7; } fprintf(treefile, "/%ld\"", qsupparr[i].qsum); column += 5; #endif } else { /* reliability value as internal label */ fprintf(treefile, "%d", consconfid[i]); column += 3; } } } /* write descending taxa */ for (i = 0; i < Maxspc; i++) { if (consbiparts[consincluded][i] == '1' || consbiparts[consincluded][i] == '3') { if (first) first = FALSE; else { fprintf(treefile, ","); column++; } if (column > 60) { column = 2; fprintf(treefile, "\n"); } column += fputid(treefile, i); } } fprintf(treefile, ");\n"); } /* writeconsensustree */ /******************/ /* prototype for recursion */ void nodecoordinates(int node); /* establish node coordinates (plotconsensustree) */ void nodecoordinates(int node) { int i, ymin, ymax, xcoordinate; /* first establish coordinates of descending nodes */ for (i = 0; i < Maxspc; i++) { if (consbiparts[node][i] == '2' || consbiparts[node][i] == '3') nodecoordinates(i); } /* then establish coordinates of descending taxa */ for (i = 0; i < Maxspc; i++) { if (consbiparts[node][i] == '1' || consbiparts[node][i] == '3') { /* y-coordinate of taxon i */ ycortax[i] = ytaxcounter; ytaxcounter = ytaxcounter - 2; } } /* then establish coordinates of this node */ ymin = 2*Maxspc - 2; ymax = 0; xcoordinate = 0; for (i = 0; i < Maxspc; i++) { if (consbiparts[node][i] == '2' || consbiparts[node][i] == '3') { if (ycor[i] > ymax) ymax = ycor[i]; if (ycor[i] < ymin) ymin = ycor[i]; if (xcor[i] > xcoordinate) xcoordinate = xcor[i]; } } for (i = 0; i < Maxspc; i++) { if (consbiparts[node][i] == '1' || consbiparts[node][i] == '3') { if (ycortax[i] > ymax) ymax = ycortax[i]; if (ycortax[i] < ymin) ymin = ycortax[i]; } } ycormax[node] = ymax; ycormin[node] = ymin; ycor[node] = (int) floor(0.5*(ymax + ymin) + 0.5); if (xcoordinate == 0) xcoordinate = 9; xcor[node] = xcoordinate + 4; } /* nodecoordinates */ /******************/ /* prototype for recursion */ void drawnode(int node, int xold); /* drawnode (plotconsensustree) */ void drawnode(int node, int xold) { int i, j; char buf[4]; /* first draw vertical line */ for (i = ycormin[node] + 1; i < ycormax[node]; i++) treepict[xcor[node]][i] = ':'; /* then draw descending nodes */ for (i = 0; i < Maxspc; i++) { if (consbiparts[node][i] == '2' || consbiparts[node][i] == '3') drawnode(i, xcor[node]); } /* then draw descending taxa */ for (i = 0; i < Maxspc; i++) { if (consbiparts[node][i] == '1' || consbiparts[node][i] == '3') { treepict[xcor[node]][ycortax[i]] = ':'; for (j = xcor[node] + 1; j < xsize-10; j++) treepict[j][ycortax[i]] = '-'; for (j = 0; j < 10; j++) treepict[xsize-10+j][ycortax[i]] = Identif[i][j]; } } /* then draw internal edge with consensus value */ treepict[xold][ycor[node]] = ':'; treepict[xcor[node]][ycor[node]] = ':'; for (i = xold + 1; i < xcor[node]-3; i++) treepict[i][ycor[node]] = '-'; sprintf(buf, "%d", consconfid[node]); if (consconfid[node] == 100) { treepict[xcor[node]-3][ycor[node]] = buf[0]; treepict[xcor[node]-2][ycor[node]] = buf[1]; treepict[xcor[node]-1][ycor[node]] = buf[2]; } else { treepict[xcor[node]-3][ycor[node]] = '-'; treepict[xcor[node]-2][ycor[node]] = buf[0]; treepict[xcor[node]-1][ycor[node]] = buf[1]; } } /* drawnode */ /******************/ /* plot consensus tree */ void plotconsensustree(FILE *plotfp) { int i, j, yroot, startree; /* star tree or no star tree */ if (consincluded == 0) { startree = TRUE; consincluded = 1; /* avoids problems with malloc */ } else startree = FALSE; /* memory for x-y-coordinates of each bipartition */ xcor = new_ivector(consincluded); ycor = new_ivector(consincluded); ycormax = new_ivector(consincluded); ycormin = new_ivector(consincluded); if (startree) consincluded = 0; /* avoids problems with malloc */ /* y-coordinates of each taxon */ ycortax = new_ivector(Maxspc); ycortax[outgroup] = 0; /* establish coordinates */ ytaxcounter = 2*Maxspc - 2; /* first establish coordinates of descending nodes */ for (i = 0; i < Maxspc; i++) { if (consbiparts[consincluded][i] == '2' || consbiparts[consincluded][i] == '3') nodecoordinates(i); } /* then establish coordinates of descending taxa */ for (i = 0; i < Maxspc; i++) { if (consbiparts[consincluded][i] == '1' || consbiparts[consincluded][i] == '3') { /* y-coordinate of taxon i */ ycortax[i] = ytaxcounter; ytaxcounter = ytaxcounter - 2; } } /* then establish length of root edge and size of whole tree */ yroot = 0; xsize = 0; for (i = 0; i < Maxspc; i++) { if (consbiparts[consincluded][i] == '2' || consbiparts[consincluded][i] == '3') { if (ycor[i] > yroot) yroot = ycor[i]; if (xcor[i] > xsize) xsize = xcor[i]; } } for (i = 0; i < Maxspc; i++) { if (consbiparts[consincluded][i] == '1' || consbiparts[consincluded][i] == '3') { if (ycortax[i] > yroot) yroot = ycortax[i]; } } if (xsize == 0) xsize = 9; /* size in x direction inclusive one blank on the left */ xsize = xsize + 6; /* change all x-labels so that (0,0) is down-left */ for (i = 0; i < consincluded; i++) xcor[i] = xsize-1-xcor[i]; /* draw tree */ treepict = new_cmatrix(xsize, 2*Maxspc-1); for (i = 0; i < xsize; i++) for (j = 0; j < 2*Maxspc-1; j++) treepict[i][j] = ' '; /* draw root */ for (i = 1; i < yroot; i++) treepict[1][i] = ':'; treepict[1][0] = ':'; for (i = 2; i < xsize - 10; i++) treepict[i][0] = '-'; for (i = 0; i < 10; i++) treepict[xsize-10+i][0] = Identif[outgroup][i]; /* then draw descending nodes */ for (i = 0; i < Maxspc; i++) { if (consbiparts[consincluded][i] == '2' || consbiparts[consincluded][i] == '3') drawnode(i, 1); } /* then draw descending taxa */ for (i = 0; i < Maxspc; i++) { if (consbiparts[consincluded][i] == '1' || consbiparts[consincluded][i] == '3') { treepict[1][ycortax[i]] = ':'; for (j = 2; j < xsize-10; j++) treepict[j][ycortax[i]] = '-'; for (j = 0; j < 10; j++) treepict[xsize-10+j][ycortax[i]] = Identif[i][j]; } } /* plot tree */ for (i = 2*Maxspc-2; i > -1; i--) { for (j = 0; j < xsize; j++) fputc(treepict[j][i], plotfp); fputc('\n', plotfp); } free_ivector(xcor); free_ivector(ycor); free_ivector(ycormax); free_ivector(ycormin); free_ivector(ycortax); free_cmatrix(treepict); } /* plotconsensustree */ tree-puzzle-5.2/src/consensus.h0000644000076400001440000001422710073365142012316 /* * consensus.h * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifndef CONSENSUS_H #define CONSENSUS_H #include "puzzle.h" #include "util.h" typedef struct { uli fullres_pro; uli fullres_con; uli partres_pro; uli partres_con; uli unres; uli missing; uli qsum; } qsupportarr_t; EXTERN cmatrix biparts; /* bipartitions of tree of current puzzling step */ EXTERN cmatrix consbiparts; /* bipartitions of majority rule consensus tree */ EXTERN int xsize; /* depth of consensus tree picture */ EXTERN ivector consconfid; /* confidence values of majority rule consensus tree */ EXTERN ivector conssizes; /* partition sizes of majority rule consensus tree */ EXTERN ivector xcor; /* x-coordinates of consensus tree nodes */ EXTERN ivector ycor; /* y-coordinates of consensus tree nodes */ EXTERN ivector ycormax; /* maximal y-coordinates of consensus tree nodes */ EXTERN ivector ycormin; /* minimal y-coordinates of consensus tree nodes */ /* splits for consensus */ EXTERN int splitlength; /* length of one entry in splitpatterns */ EXTERN uli maxbiparts; /* memory reserved for maxbiparts bipartitions */ EXTERN uli numbiparts; /* number of different bipartitions */ EXTERN int *splitsizes; /* size of all different splits of all trees */ EXTERN uli *splitcomptemp; /* temp variable to compress bipartitions coding */ EXTERN uli *splitfreqs; /* frequencies of different splits of all trees */ EXTERN uli *splitpatterns; /* all different splits of all trees */ EXTERN qsupportarr_t *qsupportarr; /* quartet support values per split */ EXTERN int consincluded; /* number of included biparts in the consensus tree */ EXTERN int consfifty; /* number of biparts >= 50% */ EXTERN int conscongruent; /* number of first incongruent bipart */ /******************************************************************************/ /* functions for computing the consensus tree */ /******************************************************************************/ /* prepare for consensus tree analysis */ void initconsensus(); /* recursive function to get bipartitions */ /* traversal should be optimazable (HAS) */ void makepart_trueID(int i, /* */ int curribrnch, /* in: current branch in traversal */ ONEEDGE *edge, /* in: tree topology */ int *edgeofleaf, /* in: ext. edge list */ int *trueID, /* in: permutation list */ cmatrix biparts, /* out: split strings, edge by edge */ int Maxspc); /* in: number of species in tree */ /* compute bipartitions of current puzzling step tree */ void computebiparts(ONEEDGE *edge, /* in: tree topology */ int *edgeofleaf, /* in: ext. edge list */ int psteprootleaf, /* virtual root from pstep */ cmatrix biparts, /* out: splits */ int outgroup, /* in: outgroup of tree */ int Maxspc); /* in: number of taxa in tree */ /* print out the bipartition n of all different splitpatterns */ void fprintfsplit(FILE *fp, /* outputfile stream */ uli n, /* split number */ uli *splitpatterns, /* splits */ int splitlength, /* number of ulis per split */ int Maxspc); /* number of taxa */ /* make new entries for new different bipartitions and count frequencies */ /* internal use: splitcomptemp */ void makenewsplitentries(cmatrix bip, /* in: split string vector */ int numspl, /* in: no. of new splits */ uli **in_splitpatterns,/* io: known compr splits */ int **in_splitsizes, /* io: kn. split sizes: '.'*/ uli **in_splitfreqs, /* io: kn. split frequences*/ uli *in_numbiparts, /* io: no. of splits so far*/ uli *in_maxbiparts, /* io: reserved memory */ int Maxspc); /* in: no. of species */ /***************************************************************************/ /* copy bipartition n of all different splitpatterns to consbiparts[k] */ void copysplit(uli n, uli *splitpatterns, int k, cmatrix consbipartsvec); /* and the quartet topologies from the ML step. Values are */ /* stored in */ /* missing parameter: quartetinfo */ void quartsupport(int splitnum, cmatrix consbipartsvec, qsupportarr_t *qsupparr); /* compute majority rule consensus tree */ void makeconsensus(uli maxnumtrees, int qsupp_optn); /* write node (writeconsensustree) */ /* missing: column */ void writenode(FILE *treefile, /* in: output stream */ int node, /* current node */ int qsupp_optn, /* 'print quartet support' flag */ qsupportarr_t *qsupparr, /* quartet support values */ int *column); /* current line position */ /* write consensus tree */ void writeconsensustree(FILE *treefile, /* in: output stream */ int qsupp_optn, /* 'print quartsupp' flag */ qsupportarr_t *qsupparr); /* quartet support values */ /* establish node coordinates (plotconsensustree) */ void nodecoordinates(int node); /* drawnode (plotconsensustree) */ void drawnode(int node, int xold); /* plot consensus tree */ void plotconsensustree(FILE *plotfp); #endif /* CONSENSUS_H */ tree-puzzle-5.2/src/recur.c0000644000076400001440000007047310073365151011416 /* * recur.c (obsolete) * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ /* initialize tree with the following starting configuration (see pstep.h) */ void inittree_recur(ONEEDGE **edge, /* out: new array of edges */ int **edgeofleaf,/* out: array of external edge ptrs */ int *rootleaf, /* out: rooting leaf (=trueID[0]) */ int Maxspc, /* in: Number of species (n) */ int Maxbrnch, /* in: Number of branches (2n-3) */ int *nextedge, /* out: next free edge index (=3) */ int *nextleaf, /* out: next free leaf index (=3) */ int *trueID) { int i, j; ONEEDGE *tmpedge; int *tmpedgeofleaf; /* allocate the memory for the whole tree */ /* allocate memory for vector with all the edges of the tree */ tmpedge = (ONEEDGE *) calloc((size_t) Maxbrnch, sizeof(ONEEDGE) ); if (tmpedge == NULL) maerror("edge in inittree"); *edge = tmpedge; /* allocate memory for tmpvector with edge numbers of leaves */ tmpedgeofleaf = (int *) calloc((size_t) Maxspc, sizeof(int) ); if (tmpedgeofleaf == NULL) maerror("edgeofleaf in inittree"); for (j = 0; j < Maxspc; j++) tmpedgeofleaf[j]=-1; *edgeofleaf = tmpedgeofleaf; /* allocate memory for all the edges the split map */ for (i = 0; i < Maxbrnch; i++) { (tmpedge)[i].cluster = (int *) calloc((size_t) Maxspc, sizeof(int) ); if (tmpedge[i].cluster == NULL) maerror("edge cluster array in inittree"); (tmpedge)[i].taxon = -1; for (j = 0; j < Maxspc; j++) (tmpedge)[i].cluster[j]=-1; /* number all edges */ tmpedge[i].numedge = i; } /* initialize tree */ *nextedge = 3; *nextleaf = 3; /* init cluster vectors: */ /* for edge 0 */ (tmpedge[0].cluster)[0] = trueID[1]; /* leaf 1 in edge cluster */ (tmpedge[0].cluster)[1] = trueID[2]; /* leaf 2 in edge cluster */ tmpedge[0].clsize = 2; /* for edge 1 */ (tmpedge[1].cluster)[0] = trueID[1]; /* leaf 0 in edge cluster */ tmpedge[1].clsize = 1; /* for edge 2 */ (tmpedge[2].cluster)[0] = trueID[2]; /* leaf 0 in edge cluster */ tmpedge[2].clsize = 1; /* interconnection */ tmpedge[0].up = NULL; tmpedge[0].downleft = &tmpedge[1]; tmpedge[0].downright = &tmpedge[2]; tmpedge[1].up = &tmpedge[0]; tmpedge[1].downleft = NULL; tmpedge[1].downright = NULL; tmpedge[2].up = &tmpedge[0]; tmpedge[2].downleft = NULL; tmpedge[2].downright = NULL; /* taxon IDs of leaves */ tmpedge[0].taxon = trueID[0]; tmpedge[1].taxon = trueID[1]; tmpedge[2].taxon = trueID[2]; /* edges of leaves */ tmpedgeofleaf[trueID[0]] = 0; tmpedgeofleaf[trueID[1]] = 1; tmpedgeofleaf[trueID[2]] = 2; /* uppest edge =: root edge*/ *rootleaf = trueID[0]; } /* inittree_recur */ /******************/ /* free memory (to be called after inittree) */ void freetree_recur(ONEEDGE *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc) /* No. of species */ { int i; /* free cluster vectors */ for (i = 0; i < 2 * Maxspc - 3; i++) { free(edge[i].cluster); } /* free tree topology */ free(edge); /* free external edge lookup vector */ free(edgeofleaf); } /* freetree_recur */ /******************/ void updatecluster_recur(ONEEDGE *curredge, /* current edge */ int wherefrom, /* direction to last curr. edge */ int newleaf, /* leaf to add to clusters */ ONEEDGE *edge, /* edge array */ int Maxspc, /* No. of species */ int Maxbrnch, /* No. of branches */ int *edgeofleaf, /* ext. edge idx array */ int in_nextedge, /* next free edge idx */ int in_nextleaf) /* next free leaf idx */ { curredge->cluster[(curredge->clsize)++] = newleaf; /* leaf is down */ if ((curredge->up) != NULL) { /* not root */ updatecluster_recur(curredge->up, DOWNLEFT, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } } /* updatecluster_recur */ /******************/ /* add next leaf on the specified edge */ void updatetreeclusters_recur(int dockedge, /* dockedge */ int newleaf, /* leaf to add to splits */ ONEEDGE *edge, /* edge array */ int Maxspc, /* No. of species */ int *edgeofleaf, /* ext. edge idx array */ int in_nextedge, /* next free edge idx */ int in_nextleaf, /* next free leaf idx */ ivector permut) { int n; /* counter */ ONEEDGE *curredge; /* edge array */ /* copy cluster dockedge -> nextedge */ for (n=0; n < edge[dockedge].clsize; n++) { (edge[in_nextedge]).cluster[n] = (edge[dockedge]).cluster[n]; } /* add newleaf new internal edge's (nextedge) cluster */ (edge[in_nextedge]).cluster[n] = newleaf; /* set new internal edge's (nextedge) cluster size */ (edge[in_nextedge]).clsize = (edge[dockedge]).clsize + 1; /* add newleaf new external edge's (nextedge+1) cluster */ (edge[in_nextedge + 1]).cluster[0] = newleaf; (edge[in_nextedge + 1]).clsize = 1; curredge = &(edge[in_nextedge]); if (curredge->up != NULL) { /* not root */ #if 0 if (((curredge->up)->downright) == curredge) { wherefrom = DOWNRIGHT; } else { wherefrom = DOWNLEFT; } #endif /* climbing up from insertion point */ updatecluster_recur(curredge->up, DOWNLEFT, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } } /* updatetreeclusters_recur */ /******************/ #if 0 /* check edge splits */ void check_recur( ONEEDGE *edge, /* edge array */ int Maxspc, /* No. of species */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *permut) { int n,m; fprintf(stderr, "Permutation: "); for (m = 0; m %d != %d>\n", m, (edge[m].taxon >= 0) ? 'e' : 'i', edge[m].taxon, edge[m].upsize, edge[m].downsize, edge[m].upsize+edge[m].downsize, nextleaf); fprintf(stderr, " UP:"); for (n = 0; n %d == %d> OK\n", m, (edge[m].taxon >= 0) ? 'e' : 'i', edge[m].taxon, edge[m].upsize, edge[m].downsize, edge[m].upsize+edge[m].downsize, nextleaf); } } } /* check_recur */ #endif /******************/ #if 0 void updatesplit_split(ONEEDGE *curredge, /* current edge */ int wherefrom, /* direction to last curr. edge */ int newleaf, /* leaf to add to splits */ ONEEDGE *edge, /* edge array */ int Maxspc, /* No. of species */ int Maxbrnch, /* No. of branches */ int *edgeofleaf, /* ext. edge idx array */ int in_nextedge, /* next free edge idx */ int in_nextleaf) /* next free leaf idx */ { switch (wherefrom) { case UP: curredge->split[(curredge->upsize)++] = newleaf; /* leaf is up */ if (curredge->downright != NULL) { /* not leaf */ updatesplit_split(curredge->downright, UP, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); updatesplit_split(curredge->downleft, UP, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } else { /* nothing to do */ return; } break; case DOWNLEFT: curredge->split[Maxspc - ++(curredge->downsize)] = newleaf; /* leaf is down */ if (curredge->downright != NULL) { /* not leaf */ updatesplit_split(curredge->downright, UP, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } if (curredge->up != NULL) { /* not root */ if ((curredge->up)->downright == curredge) { updatesplit_split(curredge->up, DOWNRIGHT, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } else { updatesplit_split(curredge->up, DOWNLEFT, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } } break; case DOWNRIGHT: curredge->split[Maxspc - ++(curredge->downsize)] = newleaf; /* leaf is down */ if (curredge->downright != NULL) { /* not leaf */ updatesplit_split(curredge->downleft, UP, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } if ((curredge->up) != NULL) { /* not root */ if ((curredge->up)->downright == curredge) { updatesplit_split(curredge->up, DOWNRIGHT, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } else { updatesplit_split(curredge->up, DOWNLEFT, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } } break; } } /* updatesplit_split */ /******************/ /* add next leaf on the specified edge */ void updatetreesplits_split(int dockedge, /* dockedge */ int newleaf, /* leaf to add to splits */ ONEEDGE *edge, /* edge array */ int Maxspc, /* No. of species */ int *edgeofleaf, /* ext. edge idx array */ int in_nextedge, /* next free edge idx */ int in_nextleaf, /* next free leaf idx */ ivector permut) { int n; /* counter */ int wherefrom; /* direction to last edge */ ONEEDGE *curredge; /* edge array */ /* copy clusters from dockedge to in_nextedge */ /* up-cluster: upsize-1 .. 0 */ for (n=(edge[dockedge].upsize) - 1; n >= 0; n--) { (edge[in_nextedge]).split[n] = (edge[dockedge]).split[n]; } (edge[in_nextedge]).upsize = (edge[dockedge]).upsize; /* down-cluster: downsize .. Maxspc-1 */ for (n=Maxspc - (edge[dockedge]).downsize; n < Maxspc; n++) { (edge[in_nextedge]).split[n] = (edge[dockedge]).split[n]; } (edge[in_nextedge]).downsize = (edge[dockedge]).downsize; /* add the new taxon to in_nextedge */ (edge[in_nextedge]).split[Maxspc - ++((edge[in_nextedge]).downsize)] = permut[in_nextleaf]; /* setup clusters for new external edge (in_nextedge+1) */ /* up-cluster: all taxa in tree */ for (n=0; n < in_nextleaf; n++) { (edge[in_nextedge+1]).split[n] = permut[n]; } (edge[in_nextedge+1]).upsize = in_nextleaf; /* down-cluster: the new taxon itself */ (edge[in_nextedge+1]).split[Maxspc-1] = permut[in_nextleaf]; (edge[in_nextedge+1]).downsize = 1; curredge = &(edge[in_nextedge]); if (curredge->up != NULL) { /* not root */ if (((curredge->up)->downright) == curredge) { wherefrom = DOWNRIGHT; } else { wherefrom = DOWNLEFT; } /* climbing up from insertion point */ updatesplit_split(curredge->up, wherefrom, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } /* climbing down to dockedge from insertion point */ updatesplit_split(&(edge[dockedge]), UP, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } /* updatetreesplits_split */ #endif /******************/ /* add next leaf on the specified edge */ void addnextleaf_recur(int dockedge, /* insert here */ ONEEDGE *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int rootleaf, /* uppest leaf */ int Maxspc, /* No. of species */ int Maxbrnch, /* No. of branches */ int *in_nextedge, /* next free edge idx */ int *in_nextleaf, /* next free leaf idx */ ivector permut) { int nextedge; int nextleaf; nextedge=*in_nextedge; nextleaf=*in_nextleaf; if (dockedge >= nextedge) { /* Trying to add leaf nextleaf to nonexisting edge dockedge */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR F TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } if (nextleaf >= Maxspc) { /* Trying to add leaf nextleaf to a tree with Maxspc leaves */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR G TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } /* necessary change in edgeofleaf if dockedge == root edge */ if (edgeofleaf[rootleaf] == dockedge) edgeofleaf[rootleaf] = nextedge; /* adding nextedge to the tree */ edge[nextedge].up = edge[dockedge].up; edge[nextedge].downleft = &edge[dockedge]; edge[nextedge].downright = &edge[nextedge+1]; edge[dockedge].up = &edge[nextedge]; /* if not root edge: connect ancestor to internal edge (nextedge) */ if (edge[nextedge].up != NULL) { if ( ((edge[nextedge].up)->downleft) == &edge[dockedge] ) (edge[nextedge].up)->downleft = &edge[nextedge]; else (edge[nextedge].up)->downright = &edge[nextedge]; } /* adding new external edge (nextedge+1) to the tree */ edge[nextedge+1].up = &edge[nextedge]; edge[nextedge+1].downleft = NULL; edge[nextedge+1].downright = NULL; edge[nextedge+1].taxon = permut[nextleaf]; edgeofleaf[permut[nextleaf]] = nextedge+1; #if 0 updatetreesplits_split(dockedge, permut[nextleaf], edge, Maxspc, edgeofleaf, nextedge, nextleaf, permut); #endif updatetreeclusters_recur(dockedge, permut[nextleaf], edge, Maxspc, edgeofleaf, nextedge, nextleaf, permut); (*in_nextedge) += 2; (*in_nextleaf) ++; } /* addnextleaf_recur */ /******************/ /* compute edge penalties using splits, if #minedges>1 choose one randomly */ void computepenalties_recur(ONEEDGE *curredge, /* edge array */ int Maxspc, /* number of taxa */ ulimatrix neighbormatr, /* neighborhood matrix */ ulivector leafpenalty, /* leaf edge penalties */ int *minedges, /* minimum edge vector */ int *howmany, /* number minimum edge */ uli *minpenalty) /* minimum penalty */ { int l, r; int lmax, rmax; int taxon; uli temp; ONEEDGE *left; /* temp edge ptr */ ONEEDGE *right; /* temp edge ptr */ if (curredge->downleft == NULL) { /* leaf edge */ taxon = curredge->taxon; #if 0 curredge->cluster[0] = taxon; curredge->clsize = 1; #endif curredge->edgeinfo = leafpenalty[taxon]; curredge->allsum = leafpenalty[taxon]; curredge->submatrsum = 0; if (*minpenalty == curredge->edgeinfo) { /* another min edge */ minedges[(*howmany)++] = curredge->numedge; } else { /* -> not same minimum */ if (*minpenalty > curredge->edgeinfo) { /* new minimum penalty */ *howmany = 1; minedges[0] = curredge->numedge; *minpenalty = curredge->edgeinfo; } /* if new minimum */ } /* same minimum */ } else { /* -> internal edge */ left = curredge->downleft; right = curredge->downright; /* descend downleft */ computepenalties_recur(left, Maxspc, neighbormatr, leafpenalty, minedges, howmany, minpenalty); /* descend downright */ computepenalties_recur(right, Maxspc, neighbormatr, leafpenalty, minedges, howmany, minpenalty); #if 0 lmax = left->clsize; for (l= 0; lcluster[l] = left->cluster[l]; } size = lmax; #endif lmax = left->clsize; rmax = right->clsize; temp = 0; for (r= 0; rcluster[r]; /* copy right cluster */ curredge->cluster[size++] = rID; #endif /* sum up sub neighborhood matrix */ for (l= 0; lcluster[l]][rID]; #endif temp += neighbormatr[left->cluster[l]][right->cluster[r]]; } } #if 0 curredge->clsize = size; #endif /* compute edge penalty */ curredge->submatrsum = 2*temp + left->submatrsum + right->submatrsum; curredge->allsum = left->allsum + right->allsum; curredge->edgeinfo = curredge->allsum - curredge->submatrsum; if (*minpenalty == curredge->edgeinfo) { /* another min edge */ minedges[(*howmany)++] = curredge->numedge; } else { /* -> not same minimum */ if (*minpenalty > curredge->edgeinfo) { /* new minimum penalty */ *howmany = 1; minedges[0] = curredge->numedge; *minpenalty = curredge->edgeinfo; } /* if new minimum */ } /* same minimum */ ; } } /* computepenalties_recur */ /******************/ /* compute edge penalties using splits, if #minedges>1 choose one randomly */ void computepenaltiestree_recur(ONEEDGE *tmpedge, /* edge array */ int *edgeofleaf, /* external edge ptrs */ int rootleaf, /* idx of uppest edge */ int nextleaf, /* next free leaf idx */ int Maxspc, /* number of taxa */ ulimatrix neighbormatr, /* neighborhood matrix */ ulivector leafpenalty, /* leaf edge penalties */ int *minedges, /* minimum edge vector */ int *out_howmany, /* number minimum edge */ uli *out_minpenalty, /* minimum penalty */ int *out_minedge) /* minimum edge */ { int rootedge; int lmax, rmax; int l, r; int howmany = 0; uli temp; ONEEDGE *left; /* temp edge ptr */ ONEEDGE *right; /* temp edge ptr */ uli minpenalty; uli submatrsum; uli allsum; uli edgeinfo; ONEEDGE *curredge; rootedge = edgeofleaf[rootleaf]; curredge = &(tmpedge[rootedge]); curredge->edgeinfo = leafpenalty[rootleaf]; /* first edge: init */ minedges[0] = rootedge; howmany = 1; minpenalty = curredge->edgeinfo; left = curredge->downleft; right = curredge->downright; /* descend downleft */ computepenalties_recur(left, Maxspc, neighbormatr, leafpenalty, minedges, &howmany, &minpenalty); /* descend downright */ computepenalties_recur(right, Maxspc, neighbormatr, leafpenalty, minedges, &howmany, &minpenalty); lmax = left->clsize; rmax = right->clsize; if ((lmax + rmax) != (nextleaf-1)) { /* root edge cluster should yield all other leaves */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR HSCL1 TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } temp = 0; for (r= 0; rcluster[l]][right->cluster[r]]; } } /* compute edge penalty */ submatrsum = 2*temp + left->submatrsum + right->submatrsum; allsum = left->allsum + right->allsum; edgeinfo = allsum - submatrsum; if ((edgeinfo) != (curredge->edgeinfo)) { /* root edge cluster should yield all other leaves */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR HSCL2 TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } #if 0 /* optimization (HAS) */ if (howmany > 1) *out_minedge = minedges[randominteger(howmany)]; else *out_minedge = minedges[0]; #endif if (howmany > 1) { /* draw random edge */ int i, k, randomnum; randomnum = randominteger(howmany) + 1; /* 1 to howmany */ i = -1; for (k = 0; k < randomnum; k++) { do { i++; } while (tmpedge[i].edgeinfo != minpenalty); *out_minedge = tmpedge[i].numedge; } } else { *out_minedge = minedges[0]; } *out_howmany = howmany; *out_minpenalty = minpenalty; } /* computepenaltiestree_recur */ /******************/ #if 0 /* compute edge penalties using splits, if #minedges>1 choose one randomly */ void computepenalties_split(ONEEDGE *tmpedge, /* edge array */ int nextedge, /* next free edge idx */ int Maxspc, /* number of taxa */ ulimatrix neighbormatr, /* neighborhood matrix */ int **out_minedges, /* minimum edge vector */ int *out_howmany, /* number minimum edge */ uli *out_minpenalty, /* minimum penalty */ int *out_minedge) /* minimum edge */ { int i; /* counter */ int a, b; int idxA, idxB; int maxUP; /* index counter for right/left split cluster */ int howmany = 0; int *minedges = *out_minedges; uli minpenalty; for (i = 0; i < nextedge; i++) { (tmpedge[i]).penalty = 0; /* reset penalty */ maxUP = (tmpedge[i]).upsize; for (idxB = Maxspc - (tmpedge[i]).downsize; idxB < Maxspc; idxB++) { b = (tmpedge[i].split)[idxB]; for (idxA = 0; idxA < maxUP; idxA++) { a = (tmpedge[i].split)[idxA]; (tmpedge[i]).penalty += neighbormatr[a][b]; } /* for all root-sided (up) taxa */ } /* for all non-root-sided (down) taxa */ if (howmany == 0) { /* first edge: init */ if (minedges == NULL) minedges = (int *) calloc((size_t) Maxspc, sizeof(int)); minedges[howmany++] = i; minpenalty = tmpedge[i].penalty; } else { /* -> all other edges */ if (minpenalty == tmpedge[i].penalty) { /* another min edge */ minedges[howmany++] = i; } else { /* -> not same minimum */ if (minpenalty > tmpedge[i].penalty) { /* new minimum penalty */ howmany = 0; minedges[howmany++] = i; minpenalty = tmpedge[i].penalty; } /* if new minimum */ } /* same minimum */ } /* if all other edges */ } /* for all edges */ *out_howmany = howmany, *out_minpenalty = minpenalty; #if 0 if (howmany > 1) *out_minedge = minedges[0]; else *out_minedge = minedges[0]; #endif } /* computepenalties_split */ #endif /******************/ /* trueID-ed (HAS) */ /* perform one single puzzling step to produce one intermediate tree */ void onepstep_recur( /* PStep (intermediate) tree topol: */ ONEEDGE **edge, /* out: new array of edges */ int **edgeofleaf, /* out: array of extern edge ptrs */ int *rootleaf, /* out: root leaf in topol, starting perm[0] */ unsigned char *quartettopols, /* in: quartetblock with all topols */ int Maxspc, /* in: Number of species (n) */ ivector permut) /* in: species permutation (trueID) */ { /* local variables: */ int Maxbrnch = (2*Maxspc)-3; /* Number of branches (2n-3) */ int nextedge; /* next free edge index (=3) */ int nextleaf; /* next free leaf index (=3) */ int minedge; /* insertion edge of minimum penalty */ uli mininfo; /* minimum penalty */ int a, b, c, i; /* quartet leaves, i to be inserted */ int idxA, idxB; int idxC, idxI; /* index counter for quartet leaves */ int chooseX, chooseY; /* end leaves of penalty path */ ONEEDGE *tmpedge; /* new array of edges */ int *tmpedgeofleaf; /* array of extern edge ptrs */ int tmprootleaf; /* root edge */ ulimatrix neighbormatr; ulivector leafpenalty; int *minedges; int howmany; neighbormatr = new_ulimatrix(Maxspc,Maxspc); leafpenalty = new_ulivector(Maxspc); minedges = (int *) calloc((size_t) Maxspc, sizeof(int)); if (minedges == NULL) maerror("minimal edge set in onepstep_recur"); /* allocate and initialize new tree topology */ inittree_recur(&tmpedge, &tmpedgeofleaf, &tmprootleaf, Maxspc, Maxbrnch, &nextedge, &nextleaf, permut); for (idxI = 3; idxI < Maxspc; idxI++) { i = permut[idxI]; /* initialize penalty neighborhood matrix + leafpenalty vector */ for (idxA = 0; idxA < nextleaf - 1; idxA++) { a = permut[idxA]; leafpenalty[a] = 0; for (idxB = idxA + 1; idxB < nextleaf; idxB++) { b = permut[idxB]; neighbormatr[a][b] = 0; neighbormatr[b][a] = 0; } } /* for all entries in the upper neighbormatr */ /* * core of quartet puzzling algorithm */ for (idxA = 0; idxA < nextleaf - 2; idxA++) { a = permut[idxA]; for (idxB = idxA + 1; idxB < nextleaf - 1; idxB++) { b = permut[idxB]; for (idxC = idxB + 1; idxC < nextleaf; idxC++) { c = permut[idxC]; /* check which two leaves out of a,b,c are closer related to each other than to leaf i according to a least squares fit of the continous Bayesian weights to the seven trivial "attractive regions". We assign a score of 1 to all edges on the penalty path between these two leaves chooseX and chooseY */ /* de-trueID-ed (HAS) */ checkquartet(a, b, c, i, &chooseX, &chooseY); (neighbormatr[chooseX][chooseY])++; } /* for all quartets q=(a,b,c,i): c */ } /* for all quartets q=(a,b,c,i): b */ } /* for all quartets q=(a,b,c,i): a */ /* symetrize penalty neighborhood matrix */ for (idxA = 0; idxA < nextleaf - 1; idxA++) { a = permut[idxA]; for (idxB = idxA + 1; idxB < nextleaf; idxB++) { b = permut[idxB]; neighbormatr[a][b] += neighbormatr[b][a]; neighbormatr[b][a] = neighbormatr[a][b]; leafpenalty[a] += neighbormatr[a][b]; leafpenalty[b] += neighbormatr[a][b]; } } /* for all entries in the upper neighbormatr */ #if 0 computepenalties_split(tmpedge, nextedge, Maxspc, neighbormatr, &minedges, &howmany, &mininfo, &minedge); #endif computepenaltiestree_recur(tmpedge, tmpedgeofleaf, tmprootleaf, nextleaf, Maxspc, neighbormatr, leafpenalty, minedges, &howmany, &mininfo, &minedge); /* add the next leaf on minedge */ addnextleaf_recur(minedge, tmpedge, tmpedgeofleaf, tmprootleaf, Maxspc, Maxbrnch, &nextedge, &nextleaf, permut); } /* adding all other leafs */ *edge = tmpedge; /* export tree topology */ *edgeofleaf = tmpedgeofleaf; /* export array of extern edge ptrs */ *rootleaf = tmprootleaf; /* export root edge */ free(minedges); free_ulimatrix(neighbormatr); free_ulivector(leafpenalty); } /* onepstep_recur */ tree-puzzle-5.2/src/ml1.c0000644000076400001440000016053410073365157010773 /* * ml1.c * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifdef HAVE_CONFIG_H # include #endif /******************************************************************************/ /* definitions and prototypes */ /******************************************************************************/ #define EXTERN extern /* prototypes */ #include #include #include #include #include "util.h" #include "ml.h" /*epe*/ #ifdef PARALLEL # include # include "ppuzzle.h" #endif #define STDOUT stdout #ifndef PARALLEL /* because printf() runs significantly faster */ /* than fprintf(stdout) on an Apple McIntosh */ /* (HS) */ # define FPRINTF printf # define STDOUTFILE #else # define FPRINTF fprintf # define STDOUTFILE STDOUT, void PP_Finalize(); /* prototype */ #endif EXTERN int printrmatr_optn; /* print rate matrix to screen */ #if 0 extern int PP_NumProcs; /*epe*/ /* might be included via ppuzzle.h ? */ extern int PP_Myid; /*epe*/ /* might be included via ppuzzle.h ? */ #endif /******************************************************************************/ /* compacting sequence data information */ /******************************************************************************/ /***************************** internal functions *****************************/ /* make all frequencies a little different */ void convfreq(dvector freqemp) { int i, j, maxi=0; double freq, maxfreq, sum; sum = 0.0; maxfreq = 0.0; for (i = 0; i < tpmradix; i++) { freq = freqemp[i]; if (freq < MINFREQ) freqemp[i] = MINFREQ; if (freq > maxfreq) { maxfreq = freq; maxi = i; } sum += freqemp[i]; } freqemp[maxi] += 1.0 - sum; for (i = 0; i < tpmradix - 1; i++) { for (j = i + 1; j < tpmradix; j++) { if (freqemp[i] == freqemp[j]) { freqemp[i] += MINFDIFF/2.0; freqemp[j] -= MINFDIFF/2.0; } } } } /* convfreq */ /* sort site patters of original input data */ void tp_radixsort(cmatrix seqchar, ivector ali, int maxspc, int maxsite, int *numptrn) { int i, j, k, l, n, pass; int *awork; int *count; awork = new_ivector(maxsite); count = new_ivector(tpmradix+1); #ifndef USE_WINDOWS for (i = 0; i < maxsite; i++) /* init alignment column order 0, 1, 2, ... */ ali[i] = i; #else alimaxsize = aliwinend - aliwinstart + 1; k = 0; for (i = aliwinstart; i < aliwinend; i++) { ali[k++] = i; #endif for (pass = maxspc - 1; pass >= 0; pass--) { /* for every taxon */ for (j = 0; j < tpmradix+1; j++) /* reset count array */ count[j] = 0; #ifndef USE_WINDOWS for (i = 0; i < maxsite; i++) /* counting bin size needed */ #else for (i = 0; i < alimaxsite; i++) /* counting bin size needed */ #endif count[(int) seqchar[pass][ali[i]]]++; for (j = 1; j < tpmradix+1; j++) /* converting bin sizes to start indices */ count[j] += count[j-1]; #ifndef USE_WINDOWS for (i = maxsite-1; i >= 0; i--) /* produce consistently sorted order of alignment columns for current species to awork */ #else for (i = alimaxsite-1; i >= 0; i--) /* produce consistently sorted order of alignment columns for current species to awork */ #endif awork[ --count[(int) seqchar[pass][ali[i]]] ] = ali[i]; for (i = 0; i < maxsite; i++) /* set intermediate order */ ali[i] = awork[i]; } free_ivector(awork); free_ivector(count); n = 1; #ifndef USE_WINDOWS for (j = 1; j < maxsite; j++) { /* counting number of site pattern */ #else for (j = 1; j < alimaxsite; j++) { /* counting number of site pattern */ #endif k = ali[j]; l = ali[j-1]; for (i = 0; i < maxspc; i++) { if (seqchar[i][l] != seqchar[i][k]) { n++; break; } } } *numptrn = n; } /* tp_radixsort */ void condenceseq(cmatrix seqchar, ivector ali, cmatrix seqconint, ivector weight, int maxspc, int maxsite, int numptrn) { int i, j, k, n; int agree_flag; /* boolean */ n = 0; k = ali[n]; #ifndef USE_WINDOWS for (i = 0; i < maxspc; i++) { #else for (i = aliwinstart - 1; i < aliwinend - 1; i++) { #endif seqconint[i][n] = seqchar[i][k]; } weight[n] = 1; Alias[k] = 0; #ifndef USE_WINDOWS for (j = 1; j < maxsite; j++) { #else for (j = 1; j < alimaxsite; j++) { #endif k = ali[j]; agree_flag = TRUE; for (i = 0; i < maxspc; i++) { if (seqconint[i][n] != seqchar[i][k]) { agree_flag = FALSE; break; } } if (agree_flag == FALSE) { n++; for (i = 0; i < maxspc; i++) { seqconint[i][n] = seqchar[i][k]; } weight[n] = 1; Alias[k] = n; } else { weight[n]++; Alias[k] = n; } } n++; if (numptrn != n) { /* Problem in condenceseq */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR A TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } } /* condenceseq */ void countconstantsites(cmatrix seqpat, ivector weight, int maxspc, int numptrn, int *numconst, int *numconstpat) { int character, s, i, constflag; *numconst = 0; *numconstpat = 0; for (s = 0; s < numptrn; s++) { /* check all patterns */ constpat[s] = FALSE; constflag = TRUE; character = seqpat[0][s]; for (i = 1; i < maxspc; i++) { if (seqpat[i][s] != character) { constflag = FALSE; break; } } /* if constant pattern (patterns with wildcards are not */ /* constant) */ if (character != tpmradix && constflag) { (*numconst) = (*numconst) + weight[s]; (*numconstpat)++; constpat[s] = TRUE; } } } /* countconstantsites */ /***************************** exported functions *****************************/ void evaluateseqs() { ivector ali; convfreq(Freqtpm); /* make all frequencies slightly different */ ali = new_ivector(Maxsite); tp_radixsort(Seqchar, ali, Maxspc, Maxsite, &Numptrn); Seqpat = new_cmatrix(Maxspc, Numptrn); constpat = new_ivector(Numptrn); Weight = new_ivector(Numptrn); condenceseq(Seqchar, ali, Seqpat, Weight, Maxspc, Maxsite, Numptrn); free_ivector(ali); countconstantsites(Seqpat, Weight, Maxspc, Numptrn, &Numconst, &Numconstpat); fracconstpat = (double) Numconstpat / (double) Numptrn; #ifndef USE_WINDOWS fracconst = (double) Numconst / (double) Maxsite; #else fracconst = (double) Numconst / (double) alimaxsite; #endif } /* evaluateseqs */ /******************************************************************************/ /* computation of Pij(t) */ /******************************************************************************/ /***************************** internal functions *****************************/ void elmhes(dmatrix a, ivector ordr, int n) { int m, j, i; double y, x; for (i = 0; i < n; i++) ordr[i] = 0; for (m = 2; m < n; m++) { x = 0.0; i = m; for (j = m; j <= n; j++) { if (fabs(a[j - 1][m - 2]) > fabs(x)) { x = a[j - 1][m - 2]; i = j; } } ordr[m - 1] = i; /* vector */ if (i != m) { for (j = m - 2; j < n; j++) { y = a[i - 1][j]; a[i - 1][j] = a[m - 1][j]; a[m - 1][j] = y; } for (j = 0; j < n; j++) { y = a[j][i - 1]; a[j][i - 1] = a[j][m - 1]; a[j][m - 1] = y; } } if (x != 0.0) { for (i = m; i < n; i++) { y = a[i][m - 2]; if (y != 0.0) { y /= x; a[i][m - 2] = y; for (j = m - 1; j < n; j++) a[i][j] -= y * a[m - 1][j]; for (j = 0; j < n; j++) a[j][m - 1] += y * a[j][i]; } } } } } /* elmhes */ void eltran(dmatrix a, dmatrix zz, ivector ordr, int n) { int i, j, m; for (i = 0; i < n; i++) { for (j = i + 1; j < n; j++) { zz[i][j] = 0.0; zz[j][i] = 0.0; } zz[i][i] = 1.0; } if (n <= 2) return; for (m = n - 1; m >= 2; m--) { for (i = m; i < n; i++) zz[i][m - 1] = a[i][m - 2]; i = ordr[m - 1]; if (i != m) { for (j = m - 1; j < n; j++) { zz[m - 1][j] = zz[i - 1][j]; zz[i - 1][j] = 0.0; } zz[i - 1][m - 1] = 1.0; } } } /* eltran */ void mcdiv(double ar, double ai, double br, double bi, double *cr, double *ci) { double s, ars, ais, brs, bis; s = fabs(br) + fabs(bi); ars = ar / s; ais = ai / s; brs = br / s; bis = bi / s; s = brs * brs + bis * bis; *cr = (ars * brs + ais * bis) / s; *ci = (ais * brs - ars * bis) / s; } /* mcdiv */ void hqr2(int n, int low, int hgh, dmatrix h, dmatrix zz, dvector wr, dvector wi) { int i, j, k, l=0, m, en, na, itn, its; double p=0, q=0, r=0, s=0, t, w, x=0, y, ra, sa, vi, vr, z=0, norm, tst1, tst2; int notlas; /* boolean */ norm = 0.0; k = 1; /* store isolated roots and compute matrix norm */ for (i = 0; i < n; i++) { for (j = k - 1; j < n; j++) norm += fabs(h[i][j]); k = i + 1; if (i + 1 < low || i + 1 > hgh) { wr[i] = h[i][i]; wi[i] = 0.0; } } en = hgh; t = 0.0; itn = n * 30; while (en >= low) { /* search for next eigenvalues */ its = 0; na = en - 1; while (en >= 1) { /* look for single small sub-diagonal element */ for (l = en; l > low; l--) { s = fabs(h[l - 2][l - 2]) + fabs(h[l - 1][l - 1]); if (s == 0.0) s = norm; tst1 = s; tst2 = tst1 + fabs(h[l - 1][l - 2]); if (tst2 == tst1) goto L100; } l = low; L100: x = h[en - 1][en - 1]; /* form shift */ if (l == en || l == na) break; if (itn == 0) { /* all eigenvalues have not converged */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR B TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } y = h[na - 1][na - 1]; w = h[en - 1][na - 1] * h[na - 1][en - 1]; /* form exceptional shift */ if (its == 10 || its == 20) { t += x; for (i = low - 1; i < en; i++) h[i][i] -= x; s = fabs(h[en - 1][na - 1]) + fabs(h[na - 1][en - 3]); x = 0.75 * s; y = x; w = -0.4375 * s * s; } its++; itn--; /* look for two consecutive small sub-diagonal elements */ for (m = en - 2; m >= l; m--) { z = h[m - 1][m - 1]; r = x - z; s = y - z; p = (r * s - w) / h[m][m - 1] + h[m - 1][m]; q = h[m][m] - z - r - s; r = h[m + 1][m]; s = fabs(p) + fabs(q) + fabs(r); p /= s; q /= s; r /= s; if (m == l) break; tst1 = fabs(p) * (fabs(h[m - 2][m - 2]) + fabs(z) + fabs(h[m][m])); tst2 = tst1 + fabs(h[m - 1][m - 2]) * (fabs(q) + fabs(r)); if (tst2 == tst1) break; } for (i = m + 2; i <= en; i++) { h[i - 1][i - 3] = 0.0; if (i != m + 2) h[i - 1][i - 4] = 0.0; } for (k = m; k <= na; k++) { notlas = (k != na); if (k != m) { p = h[k - 1][k - 2]; q = h[k][k - 2]; r = 0.0; if (notlas) r = h[k + 1][k - 2]; x = fabs(p) + fabs(q) + fabs(r); if (x != 0.0) { p /= x; q /= x; r /= x; } } if (x != 0.0) { if (p < 0.0) /* sign */ s = - sqrt(p * p + q * q + r * r); else s = sqrt(p * p + q * q + r * r); if (k != m) h[k - 1][k - 2] = -s * x; else { if (l != m) h[k - 1][k - 2] = -h[k - 1][k - 2]; } p += s; x = p / s; y = q / s; z = r / s; q /= p; r /= p; if (!notlas) { for (j = k - 1; j < n; j++) { /* row modification */ p = h[k - 1][j] + q * h[k][j]; h[k - 1][j] -= p * x; h[k][j] -= p * y; } j = (en < (k + 3)) ? en : (k + 3); /* min */ for (i = 0; i < j; i++) { /* column modification */ p = x * h[i][k - 1] + y * h[i][k]; h[i][k - 1] -= p; h[i][k] -= p * q; } /* accumulate transformations */ for (i = low - 1; i < hgh; i++) { p = x * zz[i][k - 1] + y * zz[i][k]; zz[i][k - 1] -= p; zz[i][k] -= p * q; } } else { for (j = k - 1; j < n; j++) { /* row modification */ p = h[k - 1][j] + q * h[k][j] + r * h[k + 1][j]; h[k - 1][j] -= p * x; h[k][j] -= p * y; h[k + 1][j] -= p * z; } j = (en < (k + 3)) ? en : (k + 3); /* min */ for (i = 0; i < j; i++) { /* column modification */ p = x * h[i][k - 1] + y * h[i][k] + z * h[i][k + 1]; h[i][k - 1] -= p; h[i][k] -= p * q; h[i][k + 1] -= p * r; } /* accumulate transformations */ for (i = low - 1; i < hgh; i++) { p = x * zz[i][k - 1] + y * zz[i][k] + z * zz[i][k + 1]; zz[i][k - 1] -= p; zz[i][k] -= p * q; zz[i][k + 1] -= p * r; } } } } /* for k */ } /* while infinite loop */ if (l == en) { /* one root found */ h[en - 1][en - 1] = x + t; wr[en - 1] = h[en - 1][en - 1]; wi[en - 1] = 0.0; en = na; continue; } y = h[na - 1][na - 1]; w = h[en - 1][na - 1] * h[na - 1][en - 1]; p = (y - x) / 2.0; q = p * p + w; z = sqrt(fabs(q)); h[en - 1][en - 1] = x + t; x = h[en - 1][en - 1]; h[na - 1][na - 1] = y + t; if (q >= 0.0) { /* real pair */ if (p < 0.0) /* sign */ z = p - fabs(z); else z = p + fabs(z); wr[na - 1] = x + z; wr[en - 1] = wr[na - 1]; if (z != 0.0) wr[en - 1] = x - w / z; wi[na - 1] = 0.0; wi[en - 1] = 0.0; x = h[en - 1][na - 1]; s = fabs(x) + fabs(z); p = x / s; q = z / s; r = sqrt(p * p + q * q); p /= r; q /= r; for (j = na - 1; j < n; j++) { /* row modification */ z = h[na - 1][j]; h[na - 1][j] = q * z + p * h[en - 1][j]; h[en - 1][j] = q * h[en - 1][j] - p * z; } for (i = 0; i < en; i++) { /* column modification */ z = h[i][na - 1]; h[i][na - 1] = q * z + p * h[i][en - 1]; h[i][en - 1] = q * h[i][en - 1] - p * z; } /* accumulate transformations */ for (i = low - 1; i < hgh; i++) { z = zz[i][na - 1]; zz[i][na - 1] = q * z + p * zz[i][en - 1]; zz[i][en - 1] = q * zz[i][en - 1] - p * z; } } else { /* complex pair */ wr[na - 1] = x + p; wr[en - 1] = x + p; wi[na - 1] = z; wi[en - 1] = -z; } en -= 2; } /* while en >= low */ /* backsubstitute to find vectors of upper triangular form */ if (norm != 0.0) { for (en = n; en >= 1; en--) { p = wr[en - 1]; q = wi[en - 1]; na = en - 1; if (q == 0.0) {/* real vector */ m = en; h[en - 1][en - 1] = 1.0; if (na != 0) { for (i = en - 2; i >= 0; i--) { w = h[i][i] - p; r = 0.0; for (j = m - 1; j < en; j++) r += h[i][j] * h[j][en - 1]; if (wi[i] < 0.0) { z = w; s = r; } else { m = i + 1; if (wi[i] == 0.0) { t = w; if (t == 0.0) { tst1 = norm; t = tst1; do { t = 0.01 * t; tst2 = norm + t; } while (tst2 > tst1); } h[i][en - 1] = -(r / t); } else { /* solve real equations */ x = h[i][i + 1]; y = h[i + 1][i]; q = (wr[i] - p) * (wr[i] - p) + wi[i] * wi[i]; t = (x * s - z * r) / q; h[i][en - 1] = t; if (fabs(x) > fabs(z)) h[i + 1][en - 1] = (-r - w * t) / x; else h[i + 1][en - 1] = (-s - y * t) / z; } /* overflow control */ t = fabs(h[i][en - 1]); if (t != 0.0) { tst1 = t; tst2 = tst1 + 1.0 / tst1; if (tst2 <= tst1) { for (j = i; j < en; j++) h[j][en - 1] /= t; } } } } } } else if (q > 0.0) { m = na; if (fabs(h[en - 1][na - 1]) > fabs(h[na - 1][en - 1])) { h[na - 1][na - 1] = q / h[en - 1][na - 1]; h[na - 1][en - 1] = (p - h[en - 1][en - 1]) / h[en - 1][na - 1]; } else mcdiv(0.0, -h[na - 1][en - 1], h[na - 1][na - 1] - p, q, &h[na - 1][na - 1], &h[na - 1][en - 1]); h[en - 1][na - 1] = 0.0; h[en - 1][en - 1] = 1.0; if (en != 2) { for (i = en - 3; i >= 0; i--) { w = h[i][i] - p; ra = 0.0; sa = 0.0; for (j = m - 1; j < en; j++) { ra += h[i][j] * h[j][na - 1]; sa += h[i][j] * h[j][en - 1]; } if (wi[i] < 0.0) { z = w; r = ra; s = sa; } else { m = i + 1; if (wi[i] == 0.0) mcdiv(-ra, -sa, w, q, &h[i][na - 1], &h[i][en - 1]); else { /* solve complex equations */ x = h[i][i + 1]; y = h[i + 1][i]; vr = (wr[i] - p) * (wr[i] - p); vr = vr + wi[i] * wi[i] - q * q; vi = (wr[i] - p) * 2.0 * q; if (vr == 0.0 && vi == 0.0) { tst1 = norm * (fabs(w) + fabs(q) + fabs(x) + fabs(y) + fabs(z)); vr = tst1; do { vr = 0.01 * vr; tst2 = tst1 + vr; } while (tst2 > tst1); } mcdiv(x * r - z * ra + q * sa, x * s - z * sa - q * ra, vr, vi, &h[i][na - 1], &h[i][en - 1]); if (fabs(x) > fabs(z) + fabs(q)) { h[i + 1] [na - 1] = (q * h[i][en - 1] - w * h[i][na - 1] - ra) / x; h[i + 1][en - 1] = (-sa - w * h[i][en - 1] - q * h[i][na - 1]) / x; } else mcdiv(-r - y * h[i][na - 1], -s - y * h[i][en - 1], z, q, &h[i + 1][na - 1], &h[i + 1][en - 1]); } /* overflow control */ t = (fabs(h[i][na - 1]) > fabs(h[i][en - 1])) ? fabs(h[i][na - 1]) : fabs(h[i][en - 1]); if (t != 0.0) { tst1 = t; tst2 = tst1 + 1.0 / tst1; if (tst2 <= tst1) { for (j = i; j < en; j++) { h[j][na - 1] /= t; h[j][en - 1] /= t; } } } } } } } } /* end back substitution. vectors of isolated roots */ for (i = 0; i < n; i++) { if (i + 1 < low || i + 1 > hgh) { for (j = i; j < n; j++) zz[i][j] = h[i][j]; } } /* multiply by transformation matrix to give vectors of * original full matrix. */ for (j = n - 1; j >= low - 1; j--) { m = ((j + 1) < hgh) ? (j + 1) : hgh; /* min */ for (i = low - 1; i < hgh; i++) { z = 0.0; for (k = low - 1; k < m; k++) z += zz[i][k] * h[k][j]; zz[i][j] = z; } } } return; } /* hqr2 */ /* make rate matrix with 0.01 expected substitutions per unit time */ void onepamratematrix(dmatrix a) { int i, j; double delta, temp, sum; dvector m; for (i = 0; i < tpmradix; i++) { for (j = 0; j < tpmradix; j++) { a[i][j] = Freqtpm[j]*a[i][j]; } } m = new_dvector(tpmradix); for (i = 0, sum = 0.0; i < tpmradix; i++) { for (j = 0, temp = 0.0; j < tpmradix; j++) temp += a[i][j]; m[i] = temp; /* row sum */ sum += temp*Freqtpm[i]; /* exp. rate */ } delta = 0.01 / sum; /* 0.01 subst. per unit time */ for (i = 0; i < tpmradix; i++) { for (j = 0; j < tpmradix; j++) { if (i != j) a[i][j] = delta * a[i][j]; else a[i][j] = delta * (-m[i]); } } free_dvector(m); } /* onepamratematrix */ /* print rate matrix to fp for testing purposes */ void printratematrix(FILE *fp, dmatrix a, int do_multpi) { int i, j; double sum = 0.0; double rowsum; /* fprintf(fp, "\n"); */ for (i = 0; i < tpmradix; i++) { rowsum = 0.0; fprintf(fp, "%-10s ",int2code(i)); for (j = 0; j < tpmradix; j++) { if (! do_multpi) { fprintf(fp, "%10.5f", a[i][j]); if (i != j) rowsum += a[i][j]; } else { fprintf(fp, "%10.5f", a[i][j] * Freqtpm[i]); if (i != j) rowsum += a[i][j] * Freqtpm[i]; /* if (i != j) rowsum += Freqtpm[i] * a[i][j]; */ } } sum += rowsum; fprintf(fp, " row=%10.5f\n",rowsum); } fprintf(fp, "off-diagonal sum = %10.5f\n", sum); } /* printratematrix */ void eigensystem( dvector eval, /* vector of Eigen-values */ dmatrix evec) /* vector of Eigen-vectors*/ { dvector evali, forg; dmatrix a, b; ivector ordr; int i, j, k, error; double zero; ordr = new_ivector(tpmradix); evali = new_dvector(tpmradix); forg = new_dvector(tpmradix); a = new_dmatrix(tpmradix,tpmradix); b = new_dmatrix(tpmradix,tpmradix); rtfdata(a, forg); /* get relative transition matrix and frequencies */ if (printrmatr_optn) { fprintf(stdout, "Current rate matrix R :\n"); printratematrix(stdout, a, FALSE); /* print rate matrix */ printratematrix(stdout, a, TRUE); /* print rate matrix */ fprintf(stdout, "\n"); } onepamratematrix(a); /* make 1 PAM rate matrix */ if (printrmatr_optn) { fprintf(stdout, "Current transition matrix Q (1 PAM normalized):\n"); /* print rate matrix */ printratematrix(stdout, a, FALSE); /* print rate matrix multiplied with pi */ printratematrix(stdout, a, TRUE); /* print rate matrix multiplied with pi */ } /* copy a to b */ for (i = 0; i < tpmradix; i++) for (j = 0; j < tpmradix; j++) b[i][j] = a[i][j]; elmhes(a, ordr, tpmradix); /* compute eigenvalues and eigenvectors */ eltran(a, evec, ordr, tpmradix); hqr2(tpmradix, 1, tpmradix, a, evec, eval, evali); /* check eigenvalue equation */ error = FALSE; for (j = 0; j < tpmradix; j++) { for (i = 0, zero = 0.0; i < tpmradix; i++) { for (k = 0; k < tpmradix; k++) zero += b[i][k] * evec[k][j]; zero -= eval[j] * evec[i][j]; if (fabs(zero) > 1.0e-5) error = TRUE; } } if (error) fprintf(STDOUT, "\nWARNING: Eigensystem doesn't satisfy eigenvalue equation!\n"); free_ivector(ordr); free_dvector(evali); free_dvector(forg); free_dmatrix(a); free_dmatrix(b); } /* eigensystem */ void luinverse(dmatrix inmat, dmatrix imtrx, int size) { double eps = 1.0e-20; /* ! */ int i, j, k, l, maxi=0, idx, ix, jx; double sum, tmp, maxb, aw; ivector index; double *wk; dmatrix omtrx; index = new_ivector(tpmradix); omtrx = new_dmatrix(tpmradix,tpmradix); /* copy inmat to omtrx */ for (i = 0; i < tpmradix; i++) for (j = 0; j < tpmradix; j++) omtrx[i][j] = inmat[i][j]; wk = (double *) calloc((size_t)size, sizeof(double)); aw = 1.0; for (i = 0; i < size; i++) { maxb = 0.0; for (j = 0; j < size; j++) { if (fabs(omtrx[i][j]) > maxb) maxb = fabs(omtrx[i][j]); } if (maxb == 0.0) { /* Singular matrix */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR C TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } wk[i] = 1.0 / maxb; } for (j = 0; j < size; j++) { for (i = 0; i < j; i++) { sum = omtrx[i][j]; for (k = 0; k < i; k++) sum -= omtrx[i][k] * omtrx[k][j]; omtrx[i][j] = sum; } maxb = 0.0; for (i = j; i < size; i++) { sum = omtrx[i][j]; for (k = 0; k < j; k++) sum -= omtrx[i][k] * omtrx[k][j]; omtrx[i][j] = sum; tmp = wk[i] * fabs(sum); if (tmp >= maxb) { maxb = tmp; maxi = i; } } if (j != maxi) { for (k = 0; k < size; k++) { tmp = omtrx[maxi][k]; omtrx[maxi][k] = omtrx[j][k]; omtrx[j][k] = tmp; } aw = -aw; wk[maxi] = wk[j]; } index[j] = maxi; if (omtrx[j][j] == 0.0) omtrx[j][j] = eps; if (j != size - 1) { tmp = 1.0 / omtrx[j][j]; for (i = j + 1; i < size; i++) omtrx[i][j] *= tmp; } } for (jx = 0; jx < size; jx++) { for (ix = 0; ix < size; ix++) wk[ix] = 0.0; wk[jx] = 1.0; l = -1; for (i = 0; i < size; i++) { idx = index[i]; sum = wk[idx]; wk[idx] = wk[i]; if (l != -1) { for (j = l; j < i; j++) sum -= omtrx[i][j] * wk[j]; } else if (sum != 0.0) l = i; wk[i] = sum; } for (i = size - 1; i >= 0; i--) { sum = wk[i]; for (j = i + 1; j < size; j++) sum -= omtrx[i][j] * wk[j]; wk[i] = sum / omtrx[i][i]; } for (ix = 0; ix < size; ix++) imtrx[ix][jx] = wk[ix]; } free((char *)wk); wk = NULL; free_ivector(index); free_dmatrix(omtrx); } /* luinverse */ void checkevector(dmatrix evec, dmatrix ivec, int nn) { int i, j, ia, ib, ic, error; dmatrix matx; double sum; matx = new_dmatrix(nn, nn); /* multiply matrix of eigenvectors and its inverse */ for (ia = 0; ia < nn; ia++) { for (ic = 0; ic < nn; ic++) { sum = 0.0; for (ib = 0; ib < nn; ib++) sum += evec[ia][ib] * ivec[ib][ic]; matx[ia][ic] = sum; } } /* check whether the unitary matrix is obtained */ error = FALSE; for (i = 0; i < nn; i++) { for (j = 0; j < nn; j++) { if (i == j) { if (fabs(matx[i][j] - 1.0) > 1.0e-5) error = TRUE; } else { if (fabs(matx[i][j]) > 1.0e-5) error = TRUE; } } } if (error) { fprintf(STDOUT, "\nWARNING: Inversion of eigenvector matrix not perfect!\n"); } free_dmatrix(matx); } /* checkevector */ /***************************** exported functions *****************************/ /* compute 1 PAM rate matrix, its eigensystem, and the inverse matrix thereof */ void tranprobmat() { eigensystem(Eval, Evec); /* eigensystem of 1 PAM rate matrix */ luinverse(Evec, Ievc, tpmradix); /* inverse eigenvectors are in Ievc */ checkevector(Evec, Ievc, tpmradix); /* check whether inversion was OK */ } /* tranprobmat */ /* compute P(t) */ void tprobmtrx(double arc, dmatrix tpr) { register int i, j, k; register double temp; for (k = 0; k < tpmradix; k++) { temp = exp(arc * Eval[k]); for (j = 0; j < tpmradix; j++) iexp[k][j] = Ievc[k][j] * temp; } for (i = 0; i < tpmradix; i++) { for (j = 0; j < tpmradix; j++) { temp = 0.0; for (k = 0; k < tpmradix; k++) temp += Evec[i][k] * iexp[k][j]; tpr[i][j] = fabs(temp); } } } /* tprobmtrx */ /******************************************************************************/ /* estimation of maximum likelihood distances */ /******************************************************************************/ /* compute total log-likelihood input: likelihoods for each site and non-zero rate output: total log-likelihood (incl. zero rate category) */ double comptotloglkl(dmatrix cdl) { int k, r; double loglkl, fv, fv2, sitelkl; loglkl = 0.0; fv = 1.0-fracinv; fv2 = (1.0-fracinv)/(double) numcats; if (numcats == 1) { for (k = 0; k < Numptrn; k++) { /* compute likelihood for pattern k */ sitelkl = cdl[0][k]*fv; if (constpat[k] == TRUE) sitelkl += fracinv*Freqtpm[(int) Seqpat[0][k]]; /* total log-likelihood */ loglkl += log(sitelkl)*Weight[k]; } } else { for (k = 0; k < Numptrn; k++) { /* this general routine works always but it's better to run it only when it's really necessary */ /* compute likelihood for pattern k */ sitelkl = 0.0; for (r = 0; r < numcats; r++) sitelkl += cdl[r][k]; sitelkl = fv2*sitelkl; if (constpat[k] == TRUE) sitelkl += fracinv*Freqtpm[(int) Seqpat[0][k]]; /* total log-likelihood */ loglkl += log(sitelkl)*Weight[k]; } } return loglkl; } /* comptotloglkl */ /* computes the site log-likelihoods input: likelihoods for each site and non-zero rate output: log-likelihood for each site */ void allsitelkl(dmatrix cdl, dvector aslkl) { int k, r; double fv, fv2, sitelkl; fv = 1.0-fracinv; fv2 = (1.0-fracinv)/(double) numcats; if (numcats == 1) { for (k = 0; k < Numptrn; k++) { /* compute likelihood for pattern k */ sitelkl = cdl[0][k]*fv; if (constpat[k] == TRUE) sitelkl += fracinv*Freqtpm[(int) Seqpat[0][k]]; /* site log-likelihood */ aslkl[k] = log(sitelkl); } } else { for (k = 0; k < Numptrn; k++) { /* this general routine works always but it's better to run it only when it's really necessary */ /* compute likelihood for pattern k */ sitelkl = 0.0; for (r = 0; r < numcats; r++) sitelkl += cdl[r][k]; sitelkl = fv2*sitelkl; if (constpat[k] == TRUE) sitelkl += fracinv*Freqtpm[(int) Seqpat[0][k]]; /* total log-likelihood */ aslkl[k] = log(sitelkl); } } } /* allsitelkl */ /* YYYY */ /* computes the site log-likelihoods input: likelihoods for each site and non-zero rate output: log-likelihood for each site */ void writesitelklvectorbin(FILE *outf, dvector aslkl) { int s; int dsize; dsize = sizeof(double); for (s = 0; s < Maxsite; s++) { fprintf(stdout, "%4d (%4d) %.5f \n", s, Alias[s], aslkl[Alias[s]]); if( 1 != fwrite( &(aslkl[Alias[s]]), dsize, 1, outf) ) { fprintf(stderr, "ERROR writing log-likelihood of site %d to file!!!\n", Alias[s]); # if PARALLEL PP_Finalize(); # endif exit (1); } } } /* writesitelklvectorbin */ /* outputs a name and its log-likelihoods to outf */ void writesitelklvectorphy(FILE *outf, char *name, int numsite, dvector aslkl) { int s; int dsize; dsize = sizeof(double); fprintf(outf, "%s", name); for (s = 0; s < Maxsite; s++) { if( 0 == fprintf(outf, " %.5f", aslkl[Alias[s]])) { fprintf(stderr, "ERROR writing log-likelihood of site %d for '%s' to file!!!\n", Alias[s], name); # if PARALLEL PP_Finalize(); # endif exit (1); } } fprintf(outf, "\n"); } /* writesitelklvectorphy */ /* outputs a name and its log-likelihoods to outf */ void writesitelklmatrixphy(FILE *outf, int numut, int numsite, dmatrix allslkl, dmatrix allslklc, int clock) { int t; char tmpname[20]; if (clock) fprintf(outf, " %d %d \n", 2 * numut, numsite); else fprintf(outf, " %d %d \n", numut, numsite); for (t = 0; t < numut; t++) { sprintf(tmpname, "tr%-7d ", t+1); writesitelklvectorphy(outf, tmpname, numsite, allslkl[t]); } if (clock) { for (t = 0; t < numut; t++) { sprintf(tmpname, "ctr%-7d ", t+1); writesitelklvectorphy(outf, tmpname, numsite, allslklc[t]); } } } /* writesitelklmatrixphy */ /***************************** internal functions *****************************/ /* compute negative log-likelihood of distance arc between sequences seqchi/j */ double pairlkl(double arc) { int k, r, ci, cj; double loglkl, fv, sitelkl; /* compute tpms */ for (r = 0; r < numcats; r++) /* compute tpm for rate category r */ tprobmtrx(arc*Rates[r], ltprobr[r]); loglkl = 0.0; fv = 1.0-fracinv; if (numcats == 1) { for (k = 0; k < Numptrn; k++) { /* compute likelihood for site k */ ci = seqchi[k]; cj = seqchj[k]; if (ci != tpmradix && cj != tpmradix) sitelkl = ltprobr[0][ci][cj]*fv; else sitelkl = fv; if (ci == cj && ci != tpmradix) sitelkl += fracinv*Freqtpm[ci]; /* total log-likelihood */ loglkl += log(sitelkl)*Weight[k]; } } else { for (k = 0; k < Numptrn; k++) { /* this general routine works always but it's better to run it only when it's really necessary */ /* compute likelihood for site k */ ci = seqchi[k]; cj = seqchj[k]; if (ci != tpmradix && cj != tpmradix) { sitelkl = 0.0; for (r = 0; r < numcats; r++) sitelkl += ltprobr[r][ci][cj]; sitelkl = fv*sitelkl/(double) numcats; } else sitelkl = fv; if (ci == cj && ci != tpmradix) sitelkl += fracinv*Freqtpm[ci]; /* total log-likelihood */ loglkl += log(sitelkl)*Weight[k]; } } /* return negative log-likelihood as we use a minimizing procedure */ return -loglkl; } /* pairlkl */ /***************************** exported functions *****************************/ /* maximum likelihood distance between sequence i and j */ double mldistance(int i, int j, double init) { double dist, fx, f2x; if (i == j) return 0.0; /* use old distance as start value */ /*epe dist = Distanmat[i][j];*/ dist = init; if (dist == 0.0) return 0.0; seqchi = Seqpat[i]; seqchj = Seqpat[j]; if (dist <= MINARC) dist = MINARC+1.0; if (dist >= MAXARC) dist = MAXARC-1.0; dist = onedimenmin(MINARC, dist, MAXARC, pairlkl, EPSILON_BRANCH, &fx, &f2x); return dist; } /* mldistance */ /* initialize distance matrix */ void initdistan() { int i, j, k, diff, x, y; double obs, temp; for (i = 0; i < Maxspc; i++) { Distanmat[i][i] = 0.0; for (j = i + 1; j < Maxspc; j++) { seqchi = Seqpat[i]; seqchj = Seqpat[j]; /* count observed differences */ diff = 0; for (k = 0; k < Numptrn; k++) { x = seqchi[k]; y = seqchj[k]; if (x != y && x != tpmradix && y != tpmradix) diff += Weight[k]; } if (diff == 0) Distanmat[i][j] = 0.0; else { /* use generalized JC correction to get first estimate (for the SH model the observed distance is used) */ /* observed distance */ #ifndef USE_WINDOWS obs = (double) diff / (double) Maxsite; #else obs = (double) diff / (double) alimaxsite; #endif temp = 1.0 - (double) obs*tpmradix/(tpmradix-1.0); if (temp > 0.0 && !(data_optn == 0 && SH_optn)) /* use JC corrected distance */ Distanmat[i][j] = -100.0*(tpmradix-1.0)/tpmradix * log(temp); else /* use observed distance */ Distanmat[i][j] = obs * 100.0; if (Distanmat[i][j] < MINARC) Distanmat[i][j] = MINARC; if (Distanmat[i][j] > MAXARC) Distanmat[i][j] = MAXARC; } Distanmat[j][i] = Distanmat[i][j]; } } } /* initdistan */ /* compute distance matrix */ /*epe*/ #if PARALLEL void computedistan() { int i, slaveno, loop; int xr, yr, xs=0, ys=1, numstartjobs=0, dummychunk=0; dvector startval, dummyval=new_dvector(1); ivector startlen = new_ivector(PP_NumProcs), startpoint = new_ivector(PP_NumProcs); imatrix coords = new_imatrix(PP_NumProcs, 3); schedtype sched; MPI_Status stat; loop = .5 * Maxspc * (Maxspc-1); initsched(&sched, loop, PP_NumProcs-1, 1); if (PP_NumProcs < loop) loop = PP_NumProcs-1; startlen[0] = 0; startpoint[0] = 0; /*Send first min(#numprocs, #matrix entries) matrix entries - one to each processor. If #numprocs > #matrix entries, send all matrix entries; some processors remain idle.*/ for (slaveno = 1; slaveno < PP_NumProcs; slaveno++) { if (slaveno<=loop) { unsigned int chunks = SCHEDALG_PARAM_EST(&sched); startlen[slaveno] = chunks; startpoint[slaveno] = numstartjobs; numstartjobs += chunks; coords[slaveno][0] = xs; coords[slaveno][1] = ys; coords[slaveno][2] = chunks; PP_NextCoord(&xs, &ys, chunks); } else startlen[slaveno] = 0; } startval = new_dvector(numstartjobs); PP_DMToVector(0, 1, numstartjobs, startval); MPI_Scatterv(startval, startlen, startpoint, MPI_DOUBLE, dummyval, dummychunk, MPI_DOUBLE, PP_MyMaster, PP_Comm); free_dvector(startval); /*The remaining matrix entries (if there are any) are sent to those processors that are returning results.*/ while (xspartials; while (cp->isop->isop != op) { cp = cp->isop; cpc = cp->partials; for (r = 0; r < numcats; r++) for (i = 0; i < Numptrn; i++) for (j = 0; j < tpmradix; j++) opc[r][i][j] *= cpc[r][i][j]; } } /* productpartials */ /* compute internal partial likelihoods */ void partialsinternal(Node *op) { int i, j, k, r; double sum; dcube oprob, cprob; if (clockmode == 1) { /* clocklike branch lengths */ for (r = 0; r < numcats; r++) { tprobmtrx((op->lengthc)*Rates[r], ltprobr[r]); } } else { /* non-clocklike branch lengths */ for (r = 0; r < numcats; r++) { tprobmtrx((op->length)*Rates[r], ltprobr[r]); } } oprob = op->partials; cprob = op->kinp->isop->partials; for (r = 0; r < numcats; r++) { for (k = 0; k < Numptrn; k++) { for (i = 0; i < tpmradix; i++) { sum = 0.0; for (j = 0; j < tpmradix; j++) sum += ltprobr[r][i][j] * cprob[r][k][j]; oprob[r][k][i] = sum; } } } } /* partialsinternal */ /* compute external partial likelihoods */ void partialsexternal(Node *op) { int i, j, k, r; dcube oprob; cvector dseqi; if (clockmode == 1) { /* clocklike branch lengths */ for (r = 0; r < numcats; r++) { tprobmtrx((op->lengthc)*Rates[r], ltprobr[r]); } } else { /* nonclocklike branch lengths */ for (r = 0; r < numcats; r++) { tprobmtrx((op->length)*Rates[r], ltprobr[r]); } } oprob = op->partials; dseqi = op->kinp->eprob; for (r = 0; r < numcats; r++) { for (k = 0; k < Numptrn; k++) { if ((j = dseqi[k]) == tpmradix) { for (i = 0; i < tpmradix; i++) oprob[r][k][i] = 1.0; } else { for (i = 0; i < tpmradix; i++) oprob[r][k][i] = ltprobr[r][i][j]; } } } } /* partialsexternal */ /* compute all partial likelihoods */ void initpartials(Tree *tr) { Node *cp, *rp; cp = rp = tr->rootp; do { cp = cp->isop->kinp; if (cp->isop == NULL) { /* external node */ cp = cp->kinp; /* not descen */ partialsexternal(cp); } else { /* internal node */ if (!cp->descen) { productpartials(cp->kinp->isop); partialsinternal(cp); } } } while (cp != rp); } /* initpartials */ /* compute log-likelihood given internal branch with length arc between partials partiali and partials partialj */ double intlkl(double arc) { double sumlk, slk; int r, s, i, j; dmatrix cdl; cdl = Ctree->condlkl; for (r = 0; r < numcats; r++) { tprobmtrx(arc*Rates[r], ltprobr[r]); } for (r = 0; r < numcats; r++) { for (s = 0; s < Numptrn; s++) { sumlk = 0.0; for (i = 0; i < tpmradix; i++) { slk = 0.0; for (j = 0; j < tpmradix; j++) slk += partialj[r][s][j] * ltprobr[r][i][j]; sumlk += Freqtpm[i] * partiali[r][s][i] * slk; } cdl[r][s] = sumlk; } } /* compute total log-likelihood for current tree */ Ctree->lklhd = comptotloglkl(cdl); return -(Ctree->lklhd); /* we use a minimizing procedure */ } /* intlkl */ /* optimize internal branch */ void optinternalbranch(Node *op) { double arc, fx, f2x; partiali = op->isop->partials; partialj = op->kinp->isop->partials; arc = op->length; /* nonclocklike branch lengths */ if (arc <= MINARC) arc = MINARC+1.0; if (arc >= MAXARC) arc = MAXARC-1.0; arc = onedimenmin(MINARC, arc, MAXARC, intlkl, EPSILON_BRANCH, &fx, &f2x); op->kinp->length = arc; op->length = arc; /* variance of branch length */ f2x = fabs(f2x); if (1.0/(MAXARC*MAXARC) < f2x) op->varlen = 1.0/f2x; else op->varlen = MAXARC*MAXARC; } /* optinternalbranch */ /* compute log-likelihood given external branch with length arc between partials partiali and sequence seqchi */ double extlkl(double arc) { double sumlk; int r, s, i, j; dvector opb; dmatrix cdl; cdl = Ctree->condlkl; for (r = 0; r < numcats; r++) { tprobmtrx(arc*Rates[r], ltprobr[r]); } for (r = 0; r < numcats; r++) { for (s = 0; s < Numptrn; s++) { opb = partiali[r][s]; sumlk = 0.0; if ((j = seqchi[s]) != tpmradix) { for (i = 0; i < tpmradix; i++) sumlk += (Freqtpm[i] * (opb[i] * ltprobr[r][i][j])); } else { for (i = 0; i < tpmradix; i++) sumlk += Freqtpm[i] * opb[i]; } cdl[r][s] = sumlk; } } /* compute total log-likelihood for current tree */ Ctree->lklhd = comptotloglkl(cdl); return -(Ctree->lklhd); /* we use a minimizing procedure */ } /* extlkl */ /* optimize external branch */ void optexternalbranch(Node *op) { double arc, fx, f2x; partiali = op->isop->partials; seqchi = op->kinp->eprob; arc = op->length; /* nonclocklike branch lengths */ if (arc <= MINARC) arc = MINARC+1.0; if (arc >= MAXARC) arc = MAXARC-1.0; arc = onedimenmin(MINARC, arc, MAXARC, extlkl, EPSILON_BRANCH, &fx, &f2x); op->kinp->length = arc; op->length = arc; /* variance of branch length */ f2x = fabs(f2x); if (1.0/(MAXARC*MAXARC) < f2x) op->varlen = 1.0/f2x; else op->varlen = MAXARC*MAXARC; } /* optexternalbranch */ /* finish likelihoods for each rate and site */ void finishlkl(Node *op) { int r, k, i, j; double arc, sumlk, slk; dmatrix cdl; partiali = op->isop->partials; partialj = op->kinp->isop->partials; cdl = Ctree->condlkl; arc = op->length; /* nonclocklike branch lengths */ for (r = 0; r < numcats; r++) { tprobmtrx(arc*Rates[r], ltprobr[r]); } for (r = 0; r < numcats; r++) { for (k = 0; k < Numptrn; k++) { sumlk = 0.0; for (i = 0; i < tpmradix; i++) { slk = 0.0; for (j = 0; j < tpmradix; j++) slk += partialj[r][k][j] * ltprobr[r][i][j]; sumlk += Freqtpm[i] * partiali[r][k][i] * slk; } cdl[r][k] = sumlk; } } } /* finishlkl */ /***************************** exported functions *****************************/ /* optimize branch lengths to get maximum likelihood (nonclocklike branchs) */ double optlkl(Tree *tr) { Node *cp, *rp; int nconv; double lendiff; clockmode = 0; /* nonclocklike branch lengths */ nconv = 0; Converg = FALSE; initpartials(tr); for (Numit = 1; (Numit <= MAXIT) && (!Converg); Numit++) { cp = rp = tr->rootp; do { cp = cp->isop->kinp; productpartials(cp->kinp->isop); if (cp->isop == NULL) { /* external node */ cp = cp->kinp; /* not descen */ lendiff = cp->length; optexternalbranch(cp); lendiff = fabs(lendiff - cp->length); if (lendiff < EPSILON_BRANCH) nconv++; else nconv = 0; partialsexternal(cp); } else { /* internal node */ if (cp->descen) { partialsinternal(cp); } else { lendiff = cp->length; optinternalbranch(cp); lendiff = fabs(lendiff - cp->length); if (lendiff < EPSILON_BRANCH) nconv++; else nconv = 0; /* eventually compute likelihoods for each site */ if ((cp->number == Numibrnch-1 && lendiff < EPSILON_BRANCH) || Numit == MAXIT-1) finishlkl(cp); partialsinternal(cp); } } if (nconv >= Numbrnch) { /* convergence */ Converg = TRUE; cp = rp; /* get out of here */ } } while (cp != rp); } /* compute total log-likelihood for current tree */ return comptotloglkl(tr->condlkl); } /* optlkl */ /* compute likelihood of tree for given branch lengths */ double treelkl(Tree *tr) { int i, k, r; Node *cp; dmatrix cdl; dcube prob1, prob2; double sumlk; /* compute for each site and rate log-likelihoods */ initpartials(tr); cp = tr->rootp; productpartials(cp->isop); prob1 = cp->partials; prob2 = cp->isop->partials; cdl = tr->condlkl; for (r = 0; r < numcats; r++) { for (k = 0; k < Numptrn; k++) { sumlk = 0.0; for (i = 0; i < tpmradix; i++) sumlk += Freqtpm[i] * (prob1[r][k][i] * prob2[r][k][i]); cdl[r][k] = sumlk; } } /* return total log-likelihood for current tree */ return comptotloglkl(cdl); } /* treelkl */ /******************************************************************************/ /* least-squares estimate of branch lengths */ /******************************************************************************/ /***************************** internal functions *****************************/ void luequation(dmatrix amat, dvector yvec, int size) { double eps = 1.0e-20; /* ! */ int i, j, k, l, maxi=0, idx; double sum, tmp, maxb, aw; dvector wk; ivector index; wk = new_dvector(size); index = new_ivector(size); aw = 1.0; for (i = 0; i < size; i++) { maxb = 0.0; for (j = 0; j < size; j++) { if (fabs(amat[i][j]) > maxb) maxb = fabs(amat[i][j]); } if (maxb == 0.0) { /* Singular matrix */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR D TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } wk[i] = 1.0 / maxb; } for (j = 0; j < size; j++) { for (i = 0; i < j; i++) { sum = amat[i][j]; for (k = 0; k < i; k++) sum -= amat[i][k] * amat[k][j]; amat[i][j] = sum; } maxb = 0.0; for (i = j; i < size; i++) { sum = amat[i][j]; for (k = 0; k < j; k++) sum -= amat[i][k] * amat[k][j]; amat[i][j] = sum; tmp = wk[i] * fabs(sum); if (tmp >= maxb) { maxb = tmp; maxi = i; } } if (j != maxi) { for (k = 0; k < size; k++) { tmp = amat[maxi][k]; amat[maxi][k] = amat[j][k]; amat[j][k] = tmp; } aw = -aw; wk[maxi] = wk[j]; } index[j] = maxi; if (amat[j][j] == 0.0) amat[j][j] = eps; if (j != size - 1) { tmp = 1.0 / amat[j][j]; for (i = j + 1; i < size; i++) amat[i][j] *= tmp; } } l = -1; for (i = 0; i < size; i++) { idx = index[i]; sum = yvec[idx]; yvec[idx] = yvec[i]; if (l != -1) { for (j = l; j < i; j++) sum -= amat[i][j] * yvec[j]; } else if (sum != 0.0) l = i; yvec[i] = sum; } for (i = size - 1; i >= 0; i--) { sum = yvec[i]; for (j = i + 1; j < size; j++) sum -= amat[i][j] * yvec[j]; yvec[i] = sum / amat[i][i]; } free_ivector(index); free_dvector(wk); } /* luequation */ /* least square estimation of branch lengths used for the approximate ML and as starting point in the calculation of the exact value of the ML */ /*epe*/ #if PARALLEL void lslength_par(Tree *tr, dvector distanvec, int numspc, int numibrnch, dvector Brnlength) { int i, i1, j, j1, j2, k, numbrnch, numpair, initmsg[2]; unsigned long int isum; double sum, leng, alllen, rss; ivector pths, jobsize = new_ivector(PP_NumProcs), atamt_tmp_coord = new_ivector(PP_NumProcs); dvector my_atamt_tmp, atamt_tmp; ivector IPaths; cmatrix atmt; dmatrix atamt; Node **ebp, **ibp; int numjobs, my_jobsize, my_x=0, my_y=0; if (PP_Myid != PP_MyMaster) { fprintf(STDOUT, "ERROR: Slave [%d] in parallel lslength()!\n", PP_Myid); return; } numbrnch = numspc + numibrnch; numpair = (numspc * (numspc - 1)) / 2; atmt = new_cmatrix(numbrnch, numpair); atamt = new_dmatrix(numbrnch, numbrnch); initmsg[0] = numspc; initmsg[1] = numibrnch; for (i=1; iibrnchp; IPaths = new_ivector(numibrnch*numspc); for (i=0; ipaths[j]; MPI_Bcast(IPaths, numibrnch*numspc, MPI_INT, PP_MyMaster, PP_Comm); free_ivector(IPaths); numjobs = (numbrnch * (numbrnch+1))/2; my_jobsize = numjobs/PP_NumProcs; if (numjobs%PP_NumProcs>0) my_jobsize++; jobsize[0] = my_jobsize; for (i=1; ipaths; for (j1 = 1, j = 0; j1 < numspc; j1++) { for (j2 = 0; j2 < j1; j2++, j++) { if (pths[j1] != pths[j2]) atmt[i][j] = 1; else atmt[i][j] = 0; } } } if (PP_Myid == PP_MyMaster) { my_atamt_tmp = new_dvector(my_jobsize); #ifdef VT VT_begin(1020); #endif for (i = 0; i < my_jobsize; i++) { for (k = 0, isum = 0; k < numpair; k++) if (atmt[my_x][k] && atmt[my_y][k]) isum ++; my_atamt_tmp[i] = (double) isum; PP_NextCoord_atamt(&my_x, &my_y, 1, numbrnch); } #ifdef VT VT_end(1020); #endif atamt_tmp = new_dvector(numjobs); MPI_Gatherv(my_atamt_tmp, my_jobsize, MPI_DOUBLE, atamt_tmp, jobsize, atamt_tmp_coord, MPI_DOUBLE, PP_MyMaster, PP_Comm); free_dvector(my_atamt_tmp); k=0; for (i = 0; i < numbrnch; i++) { for (j = 0; j <= i; j++) { atamt[i][j] = atamt_tmp[k]; atamt[j][i] = atamt_tmp[k]; k++; } } free_dvector(atamt_tmp); } else { #ifdef VT VT_begin(1020); #endif for (i = 0; i < numbrnch; i++) { for (j = 0; j <= i; j++) { for (k = 0, isum = 0; k < numpair; k++) if (atmt[i][k] && atmt[j][k]) isum ++; atamt[i][j] = (double) isum; atamt[j][i] = (double) isum; } } } for (i = 0; i < numbrnch; i++) { for (k = 0, sum = 0.0; k < numpair; k++) if (atmt[i][k]) sum += distanvec[k]; Brnlength[i] = sum; } luequation(atamt, Brnlength, numbrnch); for (i = 0, rss = 0.0; i < numpair; i++) { sum = distanvec[i]; for (j = 0; j < numbrnch; j++) { if (atmt[j][i] && Brnlength[j] > 0.0) sum -= Brnlength[j]; } rss += sum * sum; } tr->rssleast = sqrt(rss); alllen = 0.0; ebp = tr->ebrnchp; for (i = 0; i < numspc; i++) { leng = Brnlength[i]; alllen += leng; if (leng < MINARC) leng = MINARC; if (leng > MAXARC) leng = MAXARC; if (clockmode) { /* clock */ ebp[i]->lengthc = leng; ebp[i]->kinp->lengthc = leng; } else { /* no clock */ ebp[i]->length = leng; ebp[i]->kinp->length = leng; } Brnlength[i] = leng; } for (i = 0, j = numspc; i < numibrnch; i++, j++) { leng = Brnlength[j]; alllen += leng; if (leng < MINARC) leng = MINARC; if (leng > MAXARC) leng = MAXARC; if (clockmode) { /* clock */ ibp[i]->lengthc = leng; ibp[i]->kinp->lengthc = leng; } else { /* no clock */ ibp[i]->length = leng; ibp[i]->kinp->length = leng; } Brnlength[j] = leng; } free_cmatrix(atmt); free_dmatrix(atamt); } /* lslength_par */ #endif /* PARALLEL */ /* Ekki's sped-up version of lslength */ void lslength(Tree *tr, dvector distanvec, int numspc, int numibrnch, dvector Brnlength) { int i, i1, j, j1, j2, k, numbrnch, numpair; unsigned long int isum; double sum, leng, alllen, rss; ivector pths; cmatrix atmt; dmatrix atamt; Node **ebp, **ibp; numbrnch = numspc + numibrnch; numpair = (numspc * (numspc - 1)) / 2; atmt = new_cmatrix(numbrnch, numpair); atamt = new_dmatrix(numbrnch, numbrnch); ebp = tr->ebrnchp; ibp = tr->ibrnchp; for (i = 0; i < numspc; i++) { for (j1 = 1, j = 0; j1 < numspc; j1++) { if (j1 == i) { for (j2 = 0; j2 < j1; j2++, j++) { atmt[i][j] = 1; } } else { for (j2 = 0; j2 < j1; j2++, j++) { if (j2 == i) atmt[i][j] = 1; else atmt[i][j] = 0; } } } } for (i1 = 0, i = numspc; i1 < numibrnch; i1++, i++) { pths = ibp[i1]->paths; for (j1 = 1, j = 0; j1 < numspc; j1++) { for (j2 = 0; j2 < j1; j2++, j++) { if (pths[j1] != pths[j2]) atmt[i][j] = 1; else atmt[i][j] = 0; } } } for (i = 0; i < numbrnch; i++) { for (j = 0; j <= i; j++) { for (k = 0, isum = 0; k < numpair; k++) if (atmt[i][k] && atmt[j][k]) isum ++; atamt[i][j] = (double) isum; atamt[j][i] = (double) isum; } } for (i = 0; i < numbrnch; i++) { for (k = 0, sum = 0.0; k < numpair; k++) sum += (double) atmt[i][k] * distanvec[k]; Brnlength[i] = sum; } luequation(atamt, Brnlength, numbrnch); for (i = 0, rss = 0.0; i < numpair; i++) { sum = distanvec[i]; for (j = 0; j < numbrnch; j++) { if (atmt[j][i] && Brnlength[j] > 0.0) sum -= Brnlength[j]; } rss += sum * sum; } tr->rssleast = sqrt(rss); alllen = 0.0; for (i = 0; i < numspc; i++) { leng = Brnlength[i]; alllen += leng; if (leng < MINARC) leng = MINARC; if (leng > MAXARC) leng = MAXARC; if (clockmode) { /* clock */ ebp[i]->lengthc = leng; ebp[i]->kinp->lengthc = leng; } else { /* no clock */ ebp[i]->length = leng; ebp[i]->kinp->length = leng; } Brnlength[i] = leng; } for (i = 0, j = numspc; i < numibrnch; i++, j++) { leng = Brnlength[j]; alllen += leng; if (leng < MINARC) leng = MINARC; if (leng > MAXARC) leng = MAXARC; if (clockmode) { /* clock */ ibp[i]->lengthc = leng; ibp[i]->kinp->lengthc = leng; } else { /* no clock */ ibp[i]->length = leng; ibp[i]->kinp->length = leng; } Brnlength[j] = leng; } free_cmatrix(atmt); free_dmatrix(atamt); } /* lslength */ #if 0 /* old slow least square fit */ void lslength(Tree *tr, dvector distanvec, int numspc, int numibrnch, dvector Brnlength) { int i, i1, j, j1, j2, k, numbrnch, numpair; double sum, leng, alllen, rss; ivector pths; dmatrix atmt, atamt; Node **ebp, **ibp; numbrnch = numspc + numibrnch; numpair = (numspc * (numspc - 1)) / 2; atmt = new_dmatrix(numbrnch, numpair); atamt = new_dmatrix(numbrnch, numbrnch); ebp = tr->ebrnchp; ibp = tr->ibrnchp; for (i = 0; i < numspc; i++) { for (j1 = 1, j = 0; j1 < numspc; j1++) { if (j1 == i) { for (j2 = 0; j2 < j1; j2++, j++) { atmt[i][j] = 1.0; } } else { for (j2 = 0; j2 < j1; j2++, j++) { if (j2 == i) atmt[i][j] = 1.0; else atmt[i][j] = 0.0; } } } } for (i1 = 0, i = numspc; i1 < numibrnch; i1++, i++) { pths = ibp[i1]->paths; for (j1 = 1, j = 0; j1 < numspc; j1++) { for (j2 = 0; j2 < j1; j2++, j++) { if (pths[j1] != pths[j2]) atmt[i][j] = 1.0; else atmt[i][j] = 0.0; } } } for (i = 0; i < numbrnch; i++) { for (j = 0; j <= i; j++) { for (k = 0, sum = 0.0; k < numpair; k++) sum += atmt[i][k] * atmt[j][k]; atamt[i][j] = sum; atamt[j][i] = sum; } } for (i = 0; i < numbrnch; i++) { for (k = 0, sum = 0.0; k < numpair; k++) sum += atmt[i][k] * distanvec[k]; Brnlength[i] = sum; } luequation(atamt, Brnlength, numbrnch); for (i = 0, rss = 0.0; i < numpair; i++) { sum = distanvec[i]; for (j = 0; j < numbrnch; j++) { if (atmt[j][i] == 1.0 && Brnlength[j] > 0.0) sum -= Brnlength[j]; } rss += sum * sum; } tr->rssleast = sqrt(rss); alllen = 0.0; for (i = 0; i < numspc; i++) { leng = Brnlength[i]; alllen += leng; if (leng < MINARC) leng = MINARC; if (leng > MAXARC) leng = MAXARC; if (clockmode) { /* clock */ ebp[i]->lengthc = leng; ebp[i]->kinp->lengthc = leng; } else { /* no clock */ ebp[i]->length = leng; ebp[i]->kinp->length = leng; } Brnlength[i] = leng; } for (i = 0, j = numspc; i < numibrnch; i++, j++) { leng = Brnlength[j]; alllen += leng; if (leng < MINARC) leng = MINARC; if (leng > MAXARC) leng = MAXARC; if (clockmode) { /* clock */ ibp[i]->lengthc = leng; ibp[i]->kinp->lengthc = leng; } else { /* no clock */ ibp[i]->length = leng; ibp[i]->kinp->length = leng; } Brnlength[j] = leng; } free_dmatrix(atmt); free_dmatrix(atamt); } /* lslength */ #endif /* set branch lengths to the externally given lengths (-usebranchlen) */ void setextlength(Tree *tr, int numspc, int numibrnch, dvector Brnlength) { int i, j, numbrnch; double leng, alllen; Node **ebp, **ibp; numbrnch = numspc + numibrnch; ebp = tr->ebrnchp; ibp = tr->ibrnchp; alllen = 0.0; for (i = 0; i < numspc; i++) { if (ebp[i]->lengthset) { leng = ebp[i]->lengthext; } else { if (ebp[i]->kinp->lengthset) { leng = ebp[i]->kinp->lengthext; } else { fprintf(stderr, "WARNING: no branchlength set, defaults to 0.0!!!"); leng = 0.0; } } alllen += leng; if (leng < MINARC) leng = MINARC; if (leng > MAXARC) leng = MAXARC; if (clockmode) { /* clock */ ebp[i]->lengthc = leng; ebp[i]->kinp->lengthc = leng; } else { /* no clock */ ebp[i]->length = leng; ebp[i]->kinp->length = leng; } Brnlength[i] = leng; } for (i = 0, j = numspc; i < numibrnch; i++, j++) { if (ibp[i]->lengthset) { leng = ibp[i]->lengthext; } else { if (ibp[i]->kinp->lengthset) { leng = ibp[i]->kinp->lengthext; } else { fprintf(stderr, "WARNING: no branchlength set, defaults to 0.0!!!"); leng = 0.0; } } alllen += leng; if (leng < MINARC) leng = MINARC; if (leng > MAXARC) leng = MAXARC; if (clockmode) { /* clock */ ibp[i]->lengthc = leng; ibp[i]->kinp->lengthc = leng; } else { /* no clock */ ibp[i]->length = leng; ibp[i]->kinp->length = leng; } Brnlength[j] = leng; } } /* setextlength */ tree-puzzle-5.2/src/ml2.c0000644000076400001440000014627310073365170010773 /* * ml2.c * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifdef HAVE_CONFIG_H # include #endif #define EXTERN extern /* prototypes */ #include #include #include #include #include #include "util.h" #include "ml.h" #define STDOUT stdout #ifndef PARALLEL /* because printf() runs significantly faster */ /* than fprintf(stdout) on an Apple McIntosh */ /* (HS) */ # define FPRINTF printf # define STDOUTFILE #else # define FPRINTF fprintf # define STDOUTFILE STDOUT, void PP_Finalize(); #endif #define CHAR_PER_TREENODE 53 /* prototypes for two functions of puzzle2.c */ void fputid10(FILE *, int); int fputid(FILE *, int); /******************************************************************************/ /* user tree input */ /******************************************************************************/ /* read/convert branch length from string stream itfp */ double freadedgelength(double *length, char *ch, FILE *itfp) { long digit, ordzero; int dotread; double divisor; int minusread; ordzero = '0'; dotread = FALSE; minusread = FALSE; *length = 0.0; divisor = 1.0; *ch = fgetc(itfp); digit = (long)(*ch - ordzero); while ( ((digit <= 9) && (digit >= 0)) || *ch == '.' || *ch == '-' ) { if (*ch == '.' ) dotread = TRUE; else if (*ch == '-' ) minusread = TRUE; else { *length = *length * 10.0 + digit; if (dotread) divisor *= 10.0; } ch++; *ch = fgetc(itfp); digit = (long)(*ch - ordzero); } *length *= divisor; if (minusread) *length = -(*length); return (*length); } /* freadedgelength */ /* read/convert branch length from string *ch */ double sreadedgelength(double *length, char **ch) { long digit, ordzero; int dotread; double divisor; int minusread; ordzero = '0'; dotread = FALSE; minusread = FALSE; *length = 0.0; divisor = 1.0; /* **ch = fgetc(itfp); */ if (**ch == ':') (*ch)++; digit = (long)((**ch) - ordzero); while ( ((digit <= 9) && (digit >= 0)) || **ch == '.' || **ch == '-' ) { if (**ch == '.' ) dotread = TRUE; else if (**ch == '-' ) minusread = TRUE; else { *length = *length * 10.0 + digit; if (dotread) divisor *= 10.0; } (*ch)++; /* *ch = fgetc(itfp); */ digit = (long)((**ch) - ordzero); } *length *= 100; *length /= divisor; if (minusread) *length = -(*length); return (*length); } /* sreadedgelength */ void fremovecomment(FILE *itfp, char *ci) { int comment; if (*ci == '[') comment = 1; else { comment = 0; return; } do { *ci = fgetc(itfp); if (*ci == EOF) { fprintf(STDOUT, "\n\n\nUnable to proceed (missing ';' or ',' in tree)\n\n\n"); exit(1); } if ((*ci == ']') && comment) { comment = 0; *ci = fgetc(itfp); } if (*ci == '[') comment = 1; } while (comment); } /* fremovecomment */ /* read user tree, drop all blanks, tabs, and newlines. Drop edgelengths (after :) but keep internal labels. Check whether all pairs of brackets match. */ void getusertree(FILE *itfp, cvector tr, int maxlen, int usebranch) { int n; int brac; char ci; /* look for opening bracket */ n = 0; brac = 0; do { ci = fgetc(itfp); if (ci == EOF) { fprintf(STDOUT, "\n\n\nUnable to proceed (missing start bracket in tree)\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } if (ci == '[') fremovecomment(itfp, &ci); } while ((ci != '(')); tr[n] = ci; brac++; do { /* get next character (skip blanks, newlines, and tabs) */ do { ci = fgetc(itfp); if (ci == EOF) { fprintf(STDOUT, "\n\n\nUnable to proceed (no more characters in tree)\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } if (ci == '[') fremovecomment(itfp, &ci); } while (isspace((int) ci)); /* remove edgelengths, if not needed (HAS) */ if (ci == ':') { /* skip characters until a ,) appears */ if (!usebranch) { do { ci = fgetc(itfp); if (ci == EOF) { fprintf(STDOUT, "\n\n\nUnable to proceed (missing ';' or ',' in tree)\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } if (ci == '[') fremovecomment(itfp, &ci); } while ((ci != ',' && ci != ')') ); } else { /* if usebranch */ n++; tr[n] = ci; /* add ':' to string */ do { ci = fgetc(itfp); if (ci == EOF) { fprintf(STDOUT, "\n\n\nUnable to proceed (missing ';' or ',' in tree)\n\n\n"); exit(1); } if (ci == '[') fremovecomment(itfp, &ci); if(!isspace((int) ci) && (ci != ',') && (ci != ')')) { n++; tr[n] = ci; }; } while ((ci != ',' && ci != ')') ); } } if (ci == '(') { brac++; } if (ci == ')') { brac--; } n++; tr[n] = ci; } while ((ci != ';') && (n != maxlen-2)); if (n == maxlen-2) { fprintf(STDOUT, "\n\n\nUnable to proceed (tree description too long)\n\n\n"); fprintf(STDOUT, ">>%s<<\n\n\n", tr); # if PARALLEL PP_Finalize(); # endif exit(1); } if (brac != 0) { fprintf(STDOUT, "\n\n\nUnable to proceed (brackets don't match in tree)\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } n++; tr[n] = '\0'; } /* getusertree */ Node *internalnode(Tree *tr, char **chpp, int *ninode) { Node *xp; Node *np; Node *rp; int i, j; int dvg; int ff; int stop; int numc; char ident[100]; char idcomp[11]; char *idp; double blen; (*chpp)++; if (**chpp == '(') { /* process subgroup */ xp = internalnode(tr, chpp, ninode); xp->isop = xp; dvg = 1; while (**chpp != ')') { if (**chpp == '\0') { fprintf(STDOUT, "\n\n\nUnable to proceed (unexpected end of tree)\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } dvg++; /* insert edges around node */ np = internalnode(tr, chpp, ninode); np->isop = xp->isop; xp->isop = np; xp = np; } /* closing bracket reached */ /* read edgelength !!!! (HAS) */ (*chpp)++; if (dvg < 2) { fprintf(STDOUT, "\n\n\nUnable to proceed (only one OTU inside pair of brackets)\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } if ((*ninode) >= Maxspc-3) { /* all internal nodes already used */ fprintf(STDOUT, "\n\n\nUnable to proceed (no unrooted tree)\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } rp = tr->ibrnchp[*ninode]; rp->isop = xp->isop; xp->isop = rp; for (j = 0; j < Numspc; j++) rp->paths[j] = 0; xp = rp->isop; while (xp != rp) { for (j = 0; j < Numspc; j++) { if (xp->paths[j] == 1) rp->paths[j] = 1; } xp = xp->isop; } (*ninode)++; if ((**chpp) == ',' || (**chpp) == ')') return rp->kinp; if ((**chpp) == '\0') { fprintf(STDOUT, "\n\n\nUnable to proceed (unexpected end of tree)\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } if ((**chpp) != ':') { /* read internal label into rp->label (max. 20 characters) */ rp->label = new_cvector(21); (rp->label)[0] = '\0'; for (numc = 0; ((numc < 20) && ((**chpp) != ':')); numc++) { if ((**chpp) == ',' || (**chpp) == ')') return rp->kinp; if ((**chpp) == '\0') { fprintf(STDOUT, "\n\n\nUnable to proceed (unexpected end of tree)\n\n\n"); exit(1); } (rp->label)[numc] = **chpp; (rp->label)[numc+1] = '\0'; (*chpp)++; } /* skip the rest of the internal label */ while (((**chpp) != ',') && ((**chpp) != ')') && ((**chpp) != ':')) { (*chpp)++; if ((**chpp) == '\0') { fprintf(STDOUT, "\n\n\nUnable to proceed (unexpected end of tree)\n\n\n"); exit(1); } } } /* if ! ':' */ /* read edgelength !!!! (HAS) */ if (**chpp == ':') { (void) sreadedgelength(&blen, chpp); rp->lengthext=blen; rp->lengthset=1; rp->kinp->lengthext=blen; rp->kinp->lengthset=1; } return rp->kinp; } else { /* process species names */ /* read species name */ for (idp = ident; **chpp != ',' && **chpp != ')' && **chpp != ':' && **chpp != '\0'; (*chpp)++) { *idp++ = **chpp; } *idp = '\0'; /* look for internal number */ idcomp[10] = '\0'; for (i = 0; i < Maxspc; i++) { ff = 0; stop = FALSE; do { idcomp[ff] = Identif[i][ff]; ff++; if (idcomp[ff-1] == ' ') stop = TRUE; } while (!stop && (ff != 10)); if (stop) idcomp[ff-1] = '\0'; if (!strcmp(ident, idcomp)) { if (usedtaxa[i]) { fprintf(STDOUT, "\n\n\nUnable to proceed (multiple occurence of sequence '"); fprintf(STDOUT, "%s' in tree)\n\n\n", ident); # if PARALLEL PP_Finalize(); # endif exit(1); } usedtaxa[i] = TRUE; /* read edgelength !!!! (HAS) */ if (**chpp == ':') { (void) sreadedgelength(&blen, chpp); tr->ebrnchp[i]->lengthext=blen; tr->ebrnchp[i]->lengthset=1; tr->ebrnchp[i]->kinp->lengthext=blen; tr->ebrnchp[i]->kinp->lengthset=1; } return tr->ebrnchp[i]->kinp; } } fprintf(STDOUT, "\n\n\nUnable to proceed (unknown sequence '%s' in tree)\n\n\n", ident); # if PARALLEL PP_Finalize(); # endif exit(1); } return NULL; /* never returned but without some compilers complain */ } /* internalnode */ /* make tree structure, the tree description may contain internal labels but no edge lengths */ void constructtree(Tree *tr, cvector strtree, int usebranch) { char *chp; /* char ptr to tree string */ int ninode; /* number of internal nodes < Maxspc-3 */ int i; /* counter */ int dvg; /* degree vertex ? */ int numc; /* char counter */ Node *xp; /* last read Node/Subtree */ Node *np; /* newly read Node/Subtree */ ninode = 0; chp = strtree; usedtaxa = new_ivector(Maxspc); for (i = 0; i < Maxspc; i++) usedtaxa[i] = FALSE; xp = internalnode(tr, &chp, &ninode); xp->isop = xp; dvg = 1; while (*chp != ')') { /* look for closing bracket */ if (*chp == '\0') { fprintf(STDOUT, "\n\n\nUnable to proceed (unexpected end of tree)\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } dvg++; /* insert edges around node */ np = internalnode(tr, &chp, &ninode); np->isop = xp->isop; xp->isop = np; xp = np; } for (i = 0; i < Maxspc; i++) if (usedtaxa[i] == FALSE) { fprintf(STDOUT, "\n\n\nUnable to proceed (sequences missing in tree)\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } /* closing bracket reached */ if (dvg < 3) { fprintf(STDOUT, "\n\n\nUnable to proceed (no unrooted tree)\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } tr->rootp = xp; Numibrnch = ninode; Numbrnch = Numspc + ninode; chp++; if (*chp == ';' || *chp == '\0') { free_ivector(usedtaxa); return; } /* copy last internal label (max. 20 characters) */ xp->label = new_cvector(21); (xp->label)[0] = *chp; (xp->label)[1] = '\0'; for (numc = 1; numc < 20; numc++) { chp++; if (*chp == ';' || *chp == '\0') { free_ivector(usedtaxa); return; } else { (xp->label)[numc] = *chp; (xp->label)[numc+1] = '\0'; } } free_ivector(usedtaxa); return; } /* constructtree */ /* remove possible basal bifurcation */ void removebasalbif(cvector strtree) { int n, c, brak, cutflag, h; /* check how many OTUs on basal level */ n = 0; c = 0; brak = 0; do { if (strtree[n] == '(') brak++; if (strtree[n] == ')') brak--; if (strtree[n] == ',' && brak == 1) c++; /* number of commas in outer bracket */ n++; } while (strtree[n] != '\0'); /* if only 1 OTU inside outer bracket stop now */ if (c == 0) { fprintf(STDOUT, "\n\n\nUnable to proceed (Only 1 OTU inside outer bracket in tree)\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } /* if only 2 OTUs inside outer bracket delete second pair of brackets from the right to remove basal bifurcation */ if (c == 1) { n = 0; brak = 0; cutflag = 0; /* not yet cutted */ h = 0; do { if (strtree[n] == '(') brak++; if (strtree[n] == ')') brak--; if (brak == 2 && cutflag == 0) cutflag = 1; /* cutting */ if (brak == 1 && cutflag == 1) { cutflag = 2; /* cutted */ /* leave out internal label */ do { h++; } while (strtree[n+h] != ')' && strtree[n+h] != ','); } if (cutflag == 1) strtree[n] = strtree[n+1]; if (cutflag == 2) strtree[n-1] = strtree[n+h]; n++; } while (strtree[n] != '\0'); } } /* removebasalbif */ void makeusertree(FILE *itfp, int usebranchlen) { cvector strtree; strtree = new_cvector(CHAR_PER_TREENODE*2*Maxspc); /* for treefile */ getusertree(itfp, strtree, CHAR_PER_TREENODE*2*Maxspc, usebranchlen); removebasalbif(strtree); constructtree(Ctree, strtree, usebranchlen); free_cvector(strtree); } /* makeusertree */ /******************************************************************************/ /* memory organisation for maximum likelihood tree */ /******************************************************************************/ /* initialise new tree */ Tree *new_tree(int maxspc, int numptrn, cmatrix seqconint) { int n, i, maxibrnch; Tree *tr; Node *dp, *up; maxibrnch = maxspc - 3; heights = (Node **) calloc((size_t)(maxspc-2), sizeof(Node *)); if (heights == NULL) maerror("heights in new_tree"); tr = (Tree *) calloc((size_t)1, sizeof(Tree)); if (tr == NULL) maerror("tr in new_tree"); tr->ebrnchp = (Node **) calloc((size_t)maxspc, sizeof(Node *)); if (tr->ebrnchp == NULL) maerror("ebrnchp in new_tree"); tr->ibrnchp = (Node **) calloc((size_t)maxibrnch, sizeof(Node *)); if (tr->ibrnchp == NULL) maerror("ibrnchp in new_tree"); tr->condlkl = new_dmatrix(numcats, numptrn); for (n = 0; n < maxspc; n++) { dp = (Node *) calloc((size_t) 1, sizeof(Node)); if (dp == NULL) maerror("dp in new_tree"); up = (Node *) calloc((size_t) 1, sizeof(Node)); if (up == NULL) maerror("up in new_tree"); dp->isop = NULL; up->isop = NULL; dp->kinp = up; up->kinp = dp; dp->descen = TRUE; up->descen = FALSE; dp->number = n; up->number = n; dp->length = 0.0; up->length = 0.0; dp->lengthc = 0.0; up->lengthc = 0.0; dp->lengthext = 0.0; up->lengthext = 0.0; dp->lengthset = FALSE; up->lengthset = FALSE; dp->varlen = 0.0; up->varlen = 0.0; dp->paths = new_ivector(maxspc); up->paths = dp->paths; for (i = 0; i < maxspc; i++) dp->paths[i] = 0; dp->paths[n] = 1; dp->eprob = seqconint[n]; up->eprob = NULL; dp->partials = NULL; up->partials = new_dcube(numcats, numptrn, tpmradix); tr->ebrnchp[n] = dp; up->label = NULL; dp->label = NULL; } for (n = 0; n < maxibrnch; n++) { dp = (Node *) calloc((size_t) 1, sizeof(Node)); if (dp == NULL) maerror("dp in new_tree"); up = (Node *) calloc((size_t) 1, sizeof(Node)); if (up == NULL) maerror("up in new_tree"); dp->isop = NULL; up->isop = NULL; dp->kinp = up; up->kinp = dp; dp->descen = TRUE; up->descen = FALSE; dp->number = n; up->number = n; dp->length = 0.0; up->length = 0.0; dp->lengthc = 0.0; up->lengthc = 0.0; dp->lengthext = 0.0; up->lengthext = 0.0; dp->lengthset = FALSE; up->lengthset = FALSE; dp->varlen = 0.0; up->varlen = 0.0; dp->paths = new_ivector(maxspc); up->paths = dp->paths; for (i = 0; i < maxspc; i++) dp->paths[i] = 0; dp->eprob = NULL; up->eprob = NULL; dp->partials = new_dcube(numcats, numptrn, tpmradix); up->partials = new_dcube(numcats, numptrn, tpmradix); tr->ibrnchp[n] = dp; up->label = NULL; dp->label = NULL; } tr->rootp = NULL; /* * reserve memory for lengths of the tree branches * and for the distance matrix as a vector * (needed for LS estimation of tree branch lengths) */ Brnlength = new_dvector(2 * maxspc - 3); Distanvec = new_dvector((maxspc * (maxspc - 1)) / 2); return tr; } /* new_tree */ /* initialise quartet tree */ Tree *new_quartet(int numptrn, cmatrix seqconint) { int n, i; Tree *tr; Node *dp, *up; heights = (Node **) calloc((size_t) 2, sizeof(Node *)); if (heights == NULL) maerror("heights in new_quartet"); /* reserve memory for tree */ tr = (Tree *) calloc((size_t) 1, sizeof(Tree)); if (tr == NULL) maerror("tr in new_quartet"); tr->ebrnchp = (Node **) calloc((size_t) 4, sizeof(Node *)); if (tr->ebrnchp == NULL) maerror("ebrnchp in new_quartet"); tr->ibrnchp = (Node **) calloc((size_t) 1, sizeof(Node *)); if (tr->ibrnchp == NULL) maerror("ibrnchp in new_quartet"); tr->condlkl = new_dmatrix(numcats, numptrn); /* reserve memory for nodes */ for (n = 0; n < 4; n++) { dp = (Node *) calloc((size_t) 1, sizeof(Node)); if (dp == NULL) maerror("dp in new_quartet"); up = (Node *) calloc((size_t) 1, sizeof(Node)); if (up == NULL) maerror("dp in new_quartet"); dp->isop = NULL; dp->kinp = up; up->kinp = dp; dp->descen = TRUE; up->descen = FALSE; dp->number = n; up->number = n; dp->length = 0.0; up->length = 0.0; dp->lengthc = 0.0; up->lengthc = 0.0; dp->lengthext = 0.0; up->lengthext = 0.0; dp->lengthset = FALSE; up->lengthset = FALSE; dp->varlen = 0.0; up->varlen = 0.0; dp->paths = new_ivector(4); up->paths = dp->paths; for (i = 0; i < 4; i++) dp->paths[i] = 0; dp->paths[n] = 1; dp->eprob = seqconint[n]; /* make quartet (0,1)-(2,3) as default */ up->eprob = NULL; dp->partials = NULL; up->partials = new_dcube(numcats, numptrn, tpmradix); tr->ebrnchp[n] = dp; } /* reserve memory for internal branch */ dp = (Node *) calloc((size_t) 1, sizeof(Node)); if (dp == NULL) maerror("dp in new_quartet"); up = (Node *) calloc((size_t) 1, sizeof(Node)); if (up == NULL) maerror("dp in new_quartet"); dp->isop = tr->ebrnchp[3]->kinp; /* connect internal branch */ up->isop = tr->ebrnchp[0]->kinp; dp->kinp = up; up->kinp = dp; dp->descen = TRUE; up->descen = FALSE; dp->number = 0; up->number = 0; dp->length = 0.0; up->length = 0.0; dp->lengthc = 0.0; up->lengthc = 0.0; dp->lengthext = 0.0; up->lengthext = 0.0; dp->lengthset = FALSE; up->lengthset = FALSE; dp->varlen = 0.0; up->varlen = 0.0; dp->paths = new_ivector(4); up->paths = dp->paths; up->paths[0] = 0; up->paths[1] = 0; up->paths[2] = 1; up->paths[3] = 1; dp->eprob = NULL; up->eprob = NULL; dp->partials = new_dcube(numcats, numptrn, tpmradix); up->partials = new_dcube(numcats, numptrn, tpmradix); tr->ibrnchp[0] = dp; /* place root */ tr->rootp = up; /* connect external branches */ tr->ebrnchp[0]->kinp->isop = tr->ebrnchp[1]->kinp; tr->ebrnchp[1]->kinp->isop = tr->rootp; tr->ebrnchp[3]->kinp->isop = tr->ebrnchp[2]->kinp; tr->ebrnchp[2]->kinp->isop = tr->rootp->kinp; /* * reserve memory for lengths of the five branches * of a quartet and for the six possible distances * (needed for LS estimation of branch lengths) */ Brnlength = new_dvector(NUMQBRNCH); Distanvec = new_dvector(NUMQSPC*(NUMQSPC-1)/2); return tr; } /* new_quartet */ /* free tree memory */ void free_tree(Tree *tr, int taxa) { int n; Node *dp, *up; free(heights); free_dmatrix(tr->condlkl); for (n = 0; n < taxa; n++) { dp = tr->ebrnchp[n]; up = dp->kinp; free_ivector(dp->paths); free_dcube(up->partials); free(dp); free(up); } free(tr->ebrnchp); for (n = 0; n < (taxa-3); n++) { dp = tr->ibrnchp[n]; up = dp->kinp; free_dcube(dp->partials); free_dcube(up->partials); free_ivector(dp->paths); if (dp->label != NULL) free_cvector(dp->label); if (up->label != NULL) free_cvector(up->label); free(dp); free(up); } free(tr->ibrnchp); free(tr); free_dvector(Brnlength); /* branch lengths (for LS estimation) */ free_dvector(Distanvec); /* distances (for LS estimation) */ } /* free_tree */ /* make (a,b)-(c,d) quartet a ---+ +--- c +-----+ b ---+ +--- d species numbers range from 0 to Maxspc - 1 */ void make_quartet(int a, int b, int c, int d) { /* place sequences */ Ctree->ebrnchp[0]->eprob = Seqpat[a]; Ctree->ebrnchp[1]->eprob = Seqpat[b]; Ctree->ebrnchp[2]->eprob = Seqpat[c]; Ctree->ebrnchp[3]->eprob = Seqpat[d]; /* make distance vector */ Distanvec[0] = Distanmat[b][a]; Distanvec[1] = Distanmat[c][a]; Distanvec[2] = Distanmat[c][b]; Distanvec[3] = Distanmat[d][a]; Distanvec[4] = Distanmat[d][b]; Distanvec[5] = Distanmat[d][c]; } /* make_quartet */ /* write distance matrix as vector */ void changedistan(dmatrix distanmat, dvector distanvec, int numspc) { int i, j, k; for (k = 0, i = 1; i < numspc; i++) { for (j = 0; j < i; j++, k++) distanvec[k] = distanmat[i][j]; } } /* changedistan */ /******************************************************************************/ /* computation of maximum likelihood tree */ /******************************************************************************/ /* compute the likelihood for (a,b)-(c,d) quartet */ double quartet_lklhd(int a, int b, int c, int d) { /* reserve memory for quartet if necessary */ if (mlmode != ML_QUART) { /* no quartet tree */ if (Ctree != NULL) free_tree(Ctree, Numspc); Ctree = new_quartet(Numptrn, Seqpat); Numbrnch = NUMQBRNCH; Numibrnch = NUMQIBRNCH; Numspc = NUMQSPC; mlmode = ML_QUART; } /* make (a,b)-(c,d) quartet */ make_quartet(a,b,c,d); clockmode = 0; /* nonclocklike branch lengths */ /* least square estimate for branch length */ lslength(Ctree, Distanvec, Numspc, Numibrnch, Brnlength); /* compute likelihood */ Ctree->lklhd = optlkl(Ctree); return Ctree->lklhd; } /* quartet_lklhd */ /* compute the approximate likelihood for (a,b)-(c,d) quartet */ double quartet_alklhd(int a, int b, int c, int d) { /* reserve memory for quartet if necessary */ if (mlmode != ML_QUART) { /* no quartet tree */ if (Ctree != NULL) free_tree(Ctree, Numspc); Ctree = new_quartet(Numptrn, Seqpat); Numbrnch = NUMQBRNCH; Numibrnch = NUMQIBRNCH; Numspc = NUMQSPC; mlmode = ML_QUART; } /* make (a,b)-(c,d) quartet */ make_quartet(a,b,c,d); clockmode = 0; /* nonclocklike branch lengths */ /* least square estimate for branch length */ lslength(Ctree, Distanvec, Numspc, Numibrnch, Brnlength); /* compute likelihood */ Ctree->lklhd = treelkl(Ctree); return Ctree->lklhd; } /* quartet_alklhd */ /* read usertree from file to memory */ void readusertree(FILE *ifp, int usebranch) { /* reserve memory for tree if necessary */ if (mlmode != ML_TREE) { /* no tree */ if (Ctree != NULL) free_tree(Ctree, Numspc); Ctree = new_tree(Maxspc, Numptrn, Seqpat); Numbrnch = 2*Maxspc-3; Numibrnch = Maxspc-3; Numspc = Maxspc; mlmode = ML_TREE; } /* read tree */ makeusertree(ifp, usebranch); } /* readusertree */ /* compute the likelihood of a usertree */ double usertree_lklhd(int usebranch, int parallel) { /* be sure to have a usertree in memory and to have pairwise distances computed */ clockmode = 0; /* nonclocklike branch lengths */ if(usebranch) { /* set preset barnch lengths from usertree file */ setextlength(Ctree, Numspc, Numibrnch, Brnlength); /* compute likelihood */ Ctree->lklhd = treelkl(Ctree); } else { /* least square estimate for branch length */ changedistan(Distanmat, Distanvec, Numspc); /*epe*/ # if PARALLEL if (parallel) lslength_par(Ctree, Distanvec, Numspc, Numibrnch, Brnlength); else # endif lslength(Ctree, Distanvec, Numspc, Numibrnch, Brnlength); /* compute and optimize likelihood */ Ctree->lklhd = optlkl(Ctree); } return Ctree->lklhd; } /* usertree_lklhd */ /* compute the approximate likelihood of a usertree */ double usertree_alklhd(int usebranch, int parallel) { /* be sure to have a usertree in memory and to have pairwise distances computed */ clockmode = 0; /* nonclocklike branch lengths */ if(usebranch) { /* set preset barnch lengths from usertree file */ setextlength(Ctree, Numspc, Numibrnch, Brnlength); } else { /* least square estimate for branch length */ changedistan(Distanmat, Distanvec, Numspc); /*epe*/ # if PARALLEL if (parallel) lslength_par(Ctree, Distanvec, Numspc, Numibrnch, Brnlength); else # endif lslength(Ctree, Distanvec, Numspc, Numibrnch, Brnlength); } /* compute likelihood */ Ctree->lklhd = treelkl(Ctree); return Ctree->lklhd; } /* usertree_alklhd */ /* preparation for ML analysis */ void mlstart() { /* number of states and code length */ tpmradix = gettpmradix(); /* declare variables */ Eval = new_dvector(tpmradix); Evec = new_dmatrix(tpmradix,tpmradix); Ievc = new_dmatrix(tpmradix,tpmradix); iexp = new_dmatrix(tpmradix,tpmradix); Alias = new_ivector(Maxsite); /* process sequence information */ evaluateseqs(); bestrate = new_ivector(Numptrn); /* compute transition probability matrix */ tranprobmat(); /* non-zero rate categories */ Rates = new_dvector(numcats); updaterates(); ltprobr = new_dcube(numcats, tpmradix,tpmradix); /* compute distance matrix */ Distanmat = new_dmatrix(Maxspc, Maxspc); initdistan(); /* initialize tree pointer for quartet tree */ mlmode = ML_QUART; Ctree = new_quartet(Numptrn, Seqpat); Numbrnch = NUMQBRNCH; Numibrnch = NUMQIBRNCH; Numspc = NUMQSPC; /* computing ML distances */ /*epe computedistan() moved to inputandinit;*/ } /* mlstart */ /* recompute ml distances for quartet only */ void distupdate(int a, int b, int c, int d) { /* update distance matrix */ /* consider only entries relevant to quartet */ Distanmat[a][b] = mldistance(a, b, Distanmat[a][b]); Distanmat[b][a] = Distanmat[a][b]; Distanmat[a][c] = mldistance(a, c, Distanmat[a][c]); Distanmat[c][a] = Distanmat[a][c]; Distanmat[a][d] = mldistance(a, d, Distanmat[a][d]); Distanmat[d][a] = Distanmat[a][d]; Distanmat[b][c] = mldistance(b, c, Distanmat[b][c]); Distanmat[c][b] = Distanmat[b][c]; Distanmat[b][d] = mldistance(b, d, Distanmat[b][d]); Distanmat[d][b] = Distanmat[b][d]; Distanmat[c][d] = mldistance(c, d, Distanmat[c][d]); Distanmat[d][c] = Distanmat[c][d]; } /* distupdate */ /* cleanup after ML analysis */ void mlfinish() { if (Ctree != NULL) free_tree(Ctree, Numspc); free_ivector(bestrate); free_ivector(Alias); free_cmatrix(Seqpat); free_ivector(constpat); free_ivector(Weight); free_dmatrix(Distanmat); free_dvector(Eval); free_dmatrix(Evec); free_dmatrix(Ievc); free_dvector(Rates); free_dcube(ltprobr); free_dmatrix(iexp); } /* mlfinish */ /******************************************************************************/ /* tree output */ /******************************************************************************/ #define MAXOVER 50 #define MAXLENG 30 #define MAXCOLUMN 80 void prbranch(Node *up, int depth, int m, int maxm, ivector umbrella, ivector column, FILE *outfp) { int i, num, n, maxn, lim; Node *cp; char bch; if ((int)((clockmode ? up->lengthc : up->length) * Proportion) >= MAXOVER) { column[depth] = MAXLENG; bch = '+'; } else { column[depth] = (int)((clockmode ? up->lengthc : up->length) * Proportion) + 3; bch = '-'; } if (up->isop == NULL) { /* external branch */ num = up->number + 1; /* offset */ if (m == 1) umbrella[depth - 1] = TRUE; for (i = 0; i < depth; i++) { if (umbrella[i]) fprintf(outfp, "%*c", column[i], ':'); else fprintf(outfp, "%*c", column[i], ' '); } if (m == maxm) umbrella[depth - 1] = FALSE; for (i = 0, lim = column[depth] - 3; i < lim; i++) fputc(bch, outfp); fprintf(outfp, "-%d ", num); fputid(outfp, up->number); fputc('\n', outfp); fputc(' ', outfp); return; } num = up->number + 1 + Numspc; /* offset, internal branch */ for (cp = up->isop, maxn = 0; cp != up; cp = cp->isop, maxn++) ; for (cp = up->isop, n = 1; cp != up; cp = cp->isop, n++) { prbranch(cp->kinp, depth + 1, n, maxn, umbrella, column, outfp); if (m == 1 && n == maxn / 2) umbrella[depth - 1] = TRUE; if (n != maxn) { for (i = 0; i < depth; i++) { if (umbrella[i]) fprintf(outfp, "%*c", column[i], ':'); else fprintf(outfp, "%*c", column[i], ' '); } if (n == maxn / 2) { /* internal branch */ for (i = 0, lim = column[depth] - 3; i < lim; i++) fputc(bch, outfp); if (num < 10) fprintf(outfp, "--%d", num); else if (num < 100) fprintf(outfp, "-%2d", num); else fprintf(outfp, "%3d", num); } else { if (umbrella[depth]) fprintf(outfp, "%*c", column[depth], ':'); else fprintf(outfp, "%*c", column[depth], ' '); } fputc('\n', outfp); fputc(' ', outfp); } if (m == maxm) umbrella[depth - 1] = FALSE; } return; } /* prbranch */ void getproportion(double *proportion, dvector distanvec, int numspc) { int i, maxpair; double maxdis; maxpair = (numspc*(numspc-1))/2; maxdis = 0.0; for (i = 0; i < maxpair; i++) { if (distanvec[i] > maxdis) { maxdis = distanvec[i]; } } *proportion = (double) MAXCOLUMN / (maxdis * 3.0); if (*proportion > 1.0) *proportion = 1.0; } /* getproportion */ void prtopology(FILE *outfp) { int n, maxn, depth; ivector umbrella; ivector column; Node *cp, *rp; getproportion(&Proportion, Distanvec, Numspc); umbrella = new_ivector(Numspc); column = new_ivector(Numspc); for (n = 0; n < Numspc; n++) { umbrella[n] = FALSE; column[n] = 3; } column[0] = 1; fputc(' ', outfp); /* original code: rp = Ctree->rootp */ /* but we want to print the first group in the trichotomy as outgroup at the bottom! */ rp = Ctree->rootp->isop; for (maxn = 1, cp = rp->isop; cp != rp; cp = cp->isop, maxn++) ; depth = 1; n = 0; cp = rp; do { cp = cp->isop; n++; prbranch(cp->kinp, depth, n, maxn, umbrella, column, outfp); if (cp != rp) fprintf(outfp, "%*c\n ", column[0], ':'); } while (cp != rp); free_ivector(umbrella); free_ivector(column); } /* prtopology */ /* print unrooted tree file with branch lengths */ void fputphylogeny(FILE *fp) { Node *cp, *rp; int n; cp = rp = Ctree->rootp; putc('(', fp); n = 1; do { cp = cp->isop->kinp; if (cp->isop == NULL) { /* external node */ if (n > 60) { fprintf(fp, "\n"); n = 2; } n += fputid(fp, cp->number); fprintf(fp, ":%.5f", ((clockmode ? cp->lengthc : cp->length))*0.01); n += 7; cp = cp->kinp; } else { /* internal node */ if (cp->descen) { if (n > 60) { fprintf(fp, "\n"); n = 1; } putc('(', fp); n++; } else { putc(')', fp); n++; if (n > 60) { fprintf(fp, "\n"); n = 1; } /* internal label */ if (cp->kinp->label != NULL) { fprintf(fp, "%s", cp->kinp->label); n += strlen(cp->kinp->label); } fprintf(fp, ":%.5f", ((clockmode ? cp->lengthc : cp->length))*0.01); n += 7; } } if (!cp->descen && !cp->isop->descen && cp != rp) { putc(',', fp); /* not last subtree */ n++; } } while (cp != rp); fprintf(fp, ")"); /* internal label */ if (cp->label != NULL) fprintf(fp, "%s", cp->label); fprintf(fp, ";\n"); } /* fputphylogeny */ void resulttree(FILE *outfp, int usebranch) { int n, ne, closeflag; Node *ep, *ip; double blen; closeflag = FALSE; if (clockmode) { fprintf(outfp, "\n branch length nc/c"); fprintf(outfp, " branch length nc/c (= non-clock/clock)\n"); } else { fprintf(outfp, "\n branch length S.E."); fprintf(outfp, " branch length S.E.\n"); } for (n = 0; n < Numspc; n++) { ep = Ctree->ebrnchp[n]; ne = ep->number; fputid10(outfp, ne); fputs(" ", outfp); fprintf(outfp, "%3d", ne + 1); blen = (clockmode ? ep->lengthc : ep->length); fprintf(outfp, "%9.5f", blen*0.01); if (blen < 5.0*MINARC || blen > 0.95*MAXARC) closeflag = TRUE; if (clockmode) fprintf(outfp, "%9.3f", (ep->length)/(ep->lengthc)); else fprintf(outfp, "%9.5f", 0.01*sqrt(ep->kinp->varlen)); if (n < Numibrnch) { ip = Ctree->ibrnchp[n]; fprintf(outfp, "%8d", n + 1 + Numspc); blen = (clockmode ? ip->lengthc : ip->length); fprintf(outfp, "%9.5f", blen*0.01); if (blen < 5.0*MINARC || blen > 0.95*MAXARC) closeflag = TRUE; if (clockmode) fprintf(outfp, "%9.3f", (ip->length)/(ip->lengthc)); else fprintf(outfp, "%9.5f", 0.01*sqrt(ip->kinp->varlen)); fputc('\n', outfp); } else { if (n == Numspc - 3) { fputc('\n', outfp); } else if (n == Numspc - 2) { if (clockmode) { if (usebranch) { fprintf(outfp, " Branch lengths set by user (S.E.=0.0)!\n"); } else { if (!Convergc) fprintf(outfp, " No convergence after %d iterations!\n", Numitc); else fprintf(outfp, " %d iterations until convergence\n", Numitc); } } else { if (usebranch) { fprintf(outfp, " Branch lengths set by user (S.E.=0.0)!\n"); } else { if (!Converg) fprintf(outfp, " No convergence after %d iterations!\n", Numit); else fprintf(outfp, " %d iterations until convergence\n", Numit); } } } else if (n == Numspc - 1) { fprintf(outfp, " log L: %.2f\n", (clockmode ? Ctree->lklhdc : Ctree->lklhd)); } else { fputc('\n', outfp); } } } if(closeflag) fprintf(outfp, "\nWARNING --- at least one branch length is close to an internal boundary!\n"); } /* resulttree */ /******************************************************************************/ /* Neighbor-joining tree */ /******************************************************************************/ /* compute NJ tree and write to file */ void njtree(FILE *fp) { /* reserve memory for tree if necessary */ if (mlmode != NJ_TREE) { /* no tree */ if (Ctree != NULL) free_tree(Ctree, Numspc); Ctree = new_tree(Maxspc, Numptrn, Seqpat); Numbrnch = 2*Maxspc-3; Numibrnch = Maxspc-3; Numspc = Maxspc; mlmode = NJ_TREE; } /* construct NJ tree from distance matrix */ njdistantree(Ctree); fputphylogeny(fp); } /* njtree */ /* construct NJ tree from distance matrix */ void njdistantree(Tree *tr) { int i, j, otui=0, otuj=0, otuk, nsp2, cinode, step, restsp, k; double dij, bix, bjx, bkx, sij, smax, dnsp2; dvector r; dmatrix distan; Node **psotu, *cp, *ip, *jp, *kp; distan = new_dmatrix(Maxspc,Maxspc); for (i = 0; i < Maxspc; i++) for (j = 0; j < Maxspc; j++) distan[i][j] = Distanmat[i][j]; nsp2 = Maxspc - 2; dnsp2 = 1.0 / nsp2; r = new_dvector(Maxspc); psotu = (Node **) calloc((size_t)Maxspc, sizeof(Node *)); if (psotu == NULL) maerror("psotu in njdistantree"); /* external branches are start OTUs */ for (i = 0; i < Maxspc; i++) psotu[i] = tr->ebrnchp[i]->kinp; restsp = Maxspc; cinode = 0; /* counter for internal nodes */ for (step = 0; restsp > 3; step++) { /* NJ clustering steps */ for (i = 0; i < Maxspc; i++) { if (psotu[i] != NULL) { for (j = 0, r[i] = 0.0; j < Maxspc; j++) if (psotu[j] != NULL) r[i] += distan[i][j]; } } smax = -1.0; for (i = 0; i < Maxspc-1; i++) { if (psotu[i] != NULL) { for (j = i+1; j < Maxspc; j++) { if (psotu[j] != NULL) { sij = ( r[i] + r[j] ) * dnsp2 - distan[i][j]; if (sij > smax) { smax = sij; otui = i; otuj = j; } } } } } /* new pair: otui and otuj */ dij = distan[otui][otuj]; bix = (dij + r[otui]/nsp2 - r[otuj]/nsp2) * 0.5; bjx = dij - bix; cp = tr->ibrnchp[cinode]; ip = psotu[otui]; jp = psotu[otuj]; cp->isop = ip; ip->isop = jp; jp->isop = cp; ip->length = bix; jp->length = bjx; ip->kinp->length = ip->length; jp->kinp->length = jp->length; cp = cp->kinp; for (k = 0; k < Maxspc; k++) { if (psotu[k] != NULL && k != otui && k != otuj) { dij = (distan[otui][k] + distan[otuj][k] - distan[otui][otuj]) * 0.5; distan[otui][k] = dij; distan[k][otui] = dij; } } distan[otui][otui] = 0.0; psotu[otui] = cp; psotu[otuj] = NULL; cinode++; restsp--; nsp2--; dnsp2 = 1.0 / nsp2; } otui = otuj = otuk = -1; for (i = 0; i < Maxspc; i++) { if (psotu[i] != NULL) { if (otui == -1) otui = i; else if (otuj == -1) otuj = i; else otuk = i; } } bix = (distan[otui][otuj] + distan[otui][otuk] - distan[otuj][otuk]) * 0.5; bjx = distan[otui][otuj] - bix; bkx = distan[otui][otuk] - bix; ip = psotu[otui]; jp = psotu[otuj]; kp = psotu[otuk]; ip->isop = jp; jp->isop = kp; kp->isop = ip; ip->length = bix; jp->length = bjx; kp->length = bkx; ip->kinp->length = ip->length; jp->kinp->length = jp->length; kp->kinp->length = kp->length; tr->rootp = kp; free_dvector(r); free_dmatrix(distan); free((Node *) psotu); } /* njdistantree */ /******************************************************************************/ /* find best assignment of rate categories */ /******************************************************************************/ /* find best assignment of rate categories */ #if 0 void findbestratecombination(Tree *ctree, /* Ctree */ cmatrix Seqpat, dvector Freqtpm, double fracinv, ivector constpat, ivector bestrate, int bestratefound, int ncats) /* numcats */ #endif void findbestratecombination() { int k, u; double bestvalue, fv2; dvector catprob; dmatrix cdl; /* cdl = ctree->condlkl; */ cdl = Ctree->condlkl; /* catprob = new_dvector(ncats+1); */ catprob = new_dvector(numcats+1); /* fv2 = (1.0-fracinv)/(double) ncats; */ fv2 = (1.0-fracinv)/(double) numcats; for (k = 0; k < Numptrn; k++) { /* zero rate */ if (constpat[k] == TRUE) catprob[0] = fracinv*Freqtpm[(int) Seqpat[0][k]]; else catprob[0] = 0.0; /* non-zero-rates */ /* for (u = 1; u < ncats+1; u++) { */ for (u = 1; u < numcats+1; u++) { catprob[u] = fv2*cdl[u-1][k]; } /* find best */ bestvalue = catprob[0]; bestrate[k] = 0; /* for (u = 1; u < ncats+1; u++) */ for (u = 1; u < numcats+1; u++) if (catprob[u] >= bestvalue) { bestvalue = catprob[u]; bestrate[k] = u; } } /* for all column patterns */ free_dvector(catprob); bestratefound = 1; } /* findbestratecombination */ /* print best assignment of rate categories */ void printbestratecombination(FILE *fp) { int s, k; #ifndef USE_WINDOWS for (s = 0; s < Maxsite; s++) { #else for (s = 0; s < alimaxsite; s++) { #endif k = Alias[s]; fprintf(fp, "%2d", bestrate[k]); if ((s+1) % 30 == 0) fprintf(fp, "\n"); else if ((s+1) % 10 == 0) fprintf(fp, " "); } if (s % 70 != 0) fprintf(fp, "\n"); } /* printbestratecombination */ #if 0 # define MLUNIFORMRATE 0 # define MLGAMMARATE 1 # define MLTWORATE 2 # define MLMIXEDRATE 3 #endif void printbestratecombinationtofile(FILE *fp, int rhettype) { int s; char name[11]; switch(rhettype) { case GAMMARATE: sprintf(name, "%drates", numcats); break;; case MIXEDRATE: sprintf(name, "1inv+%d", numcats); break;; case TWORATE: sprintf(name, "1inv+1var"); break;; default: /* UNIFORMRATE */ sprintf(name, "uniform"); } #ifndef USE_WINDOWS fprintf(fp, " 1 %d %d \n", Maxsite, numcats); fprintf(fp, "%-10s", name); for (s = 0; s < Maxsite; s++) { #else fprintf(fp, " 1 %d %d \n", alimaxsite, numcats); fprintf(fp, "%-10s", name); for (s = 0; s < alimaxsite; s++) { #endif if (rhettype != UNIFORMRATE) fprintf(fp, " %.5f", Rates[bestrate[Alias[s]] - 1]); else fprintf(fp, " 1.0"); } fprintf(fp, "\n"); } /* printbestratecombination */ #if 0 # undef MLUNIFORMRATE # undef MLGAMMARATE # undef MLTWORATE # undef MLMIXEDRATE #endif /******************************************************************************/ /* computation of clocklike branch lengths */ /******************************************************************************/ /* checks wether e is a valid edge specification */ int checkedge(int e) { /* there are Numspc external branches: 0 - Numspc-1 there are Numibrnch internal branches: Numspc - Numspc+Numibrnch-1 */ if (e < 0) return FALSE; if (e < Numspc+Numibrnch) return TRUE; else return FALSE; } /* checkedge */ /* print topology of subtree */ void fputsubstree(FILE *fp, Node *ip) { Node *cp; if (ip->isop == NULL) { /* terminal nodes */ numtc += fputid(fp, ip->number); } else { cp = ip; fprintf(fp, "("); numtc += 1; do { cp = cp->isop->kinp; if (cp->isop == NULL) { /* external node */ numtc += fputid(fp, cp->number); fprintf(fp, ":%.5f", (cp->lengthc)*0.01); numtc += 7; cp = cp->kinp; } else { /* internal node */ if (cp->height > 0.0) { fprintf(fp, "("); numtc += 1; } else if (cp->height < 0.0) { fprintf(fp, ")"); numtc += 1; if (numtc > 60) { fprintf(fp, "\n"); numtc = 1; } /* internal label */ if (cp->kinp->label != NULL) { fprintf(fp, "%s", cp->kinp->label); numtc += strlen(cp->kinp->label); } if (numtc > 60) { fprintf(fp, "\n"); numtc = 1; } fprintf(fp, ":%.5f", (cp->lengthc)*0.01); numtc += 6; if (numtc > 60) { fprintf(fp, "\n"); numtc = 1; } } } if (cp->height <= 0.0 && cp->isop->height <= 0.0 && cp->isop != ip) { putc(',', fp); /* not last subtree */ numtc += 1; if (numtc > 60) { fprintf(fp, "\n"); numtc = 1; } } } while (cp->isop != ip); fprintf(fp, ")"); numtc += 1; } if (numtc > 60) { fprintf(fp, "\n"); numtc = 1; } } /* fputsubstree */ /* print rooted tree file */ void fputrooted(FILE *fp, int e) { Node *rootbr; /* to be called only after clocklike branch lengths have been computed */ /* pointer to root branch */ if (e < Numspc) rootbr = Ctree->ebrnchp[e]; else rootbr = Ctree->ibrnchp[e - Numspc]; fprintf(fp, "("); numtc = 2; fputsubstree(fp, rootbr); /* internal label */ if (rootbr->label != NULL) { fprintf(fp, "%s", rootbr->label); numtc += strlen(rootbr->label); } if (numtc > 60) { fprintf(fp, "\n"); numtc = 1; } fprintf(fp, ":%.5f,", (hroot - rootbr->height)*0.01); numtc += 7; if (numtc > 60) { fprintf(fp, "\n"); numtc = 1; } fputsubstree(fp, rootbr->kinp); /* internal label */ if (rootbr->kinp->label != NULL) { fprintf(fp, "%s", rootbr->kinp->label); numtc += strlen(rootbr->kinp->label); } if (numtc > 60) { fprintf(fp, "\n"); numtc = 1; } fprintf(fp, ":%.5f);\n", (hroot - rootbr->kinp->height)*0.01); } /* fputrooted */ /* finds heights in subtree */ void findheights(Node *ip) { Node *cp, *rp; if (ip->isop != NULL) { /* forget terminal nodes */ cp = ip; /* initialise node */ cp->height = 1.0; /* up */ rp = cp; while (rp->isop != cp) { rp = rp->isop; rp->height = -1.0; /* down */ } do { cp = cp->isop->kinp; if (cp->isop == NULL) { /* external node */ cp = cp->kinp; } else { /* internal node */ if (cp->height == 0.0) { /* node not yet visited */ cp->height = 1.0; /* up */ rp = cp; while (rp->isop != cp) { rp = rp->isop; rp->height = -1.0; /* down */ } } else if (cp->kinp->height == 1.0) { /* cp->kinp is next height pointer */ heights[Numhts] = cp->kinp; Numhts++; } } } while (cp->isop != ip); /* ip is last height pointer */ heights[Numhts] = ip; Numhts++; } } /* findheights */ /* initialise clocklike branch lengths (with root on edge e) */ void initclock(int e) { int n, h, count; Node *cp, *rp; double sum, minh, aveh, len; /* be sure to have a Ctree in memory and to have pairwise distances computed */ clockmode = 1; /* clocklike branch lengths */ /* least square estimate for branch length */ changedistan(Distanmat, Distanvec, Numspc); lslength(Ctree, Distanvec, Numspc, Numibrnch, Brnlength); /* pointer to root branch */ if (e < Numspc) rootbr = Ctree->ebrnchp[e]; else rootbr = Ctree->ibrnchp[e - Numspc]; /* clear all heights */ for (n = 0; n < Numspc; n++) { Ctree->ebrnchp[n]->height = 0.0; Ctree->ebrnchp[n]->kinp->height = 0.0; Ctree->ebrnchp[n]->varheight = 0.0; Ctree->ebrnchp[n]->kinp->varheight = 0.0; if (n < Numibrnch) { Ctree->ibrnchp[n]->height = 0.0; Ctree->ibrnchp[n]->kinp->height = 0.0; Ctree->ibrnchp[n]->varheight = 0.0; Ctree->ibrnchp[n]->kinp->varheight = 0.0; } } /* collect pointers to height nodes */ Numhts = 0; findheights(rootbr); /* one side */ findheights(rootbr->kinp); /* other side */ /* assign preliminary approximate heights and corresponding branch lengths */ for (h = 0; h < Numhts; h++) { cp = rp = heights[h]; sum = 0; count = 0; minh = 0.0; while (rp->isop != cp) { count++; rp = rp->isop; sum += rp->lengthc + rp->kinp->height; if (rp->kinp->height > minh) minh = rp->kinp->height; } aveh = sum / (double) count; if (aveh < minh + MINARC) aveh = minh + MINARC; cp->height = aveh; rp = cp; while (rp->isop != cp) { rp = rp->isop; len = aveh - rp->kinp->height; rp->kinp->lengthc = len; rp->lengthc = len; } } if (rootbr->height > rootbr->kinp->height) minh = rootbr->height; else minh = rootbr->kinp->height; aveh = 0.5*(rootbr->lengthc + rootbr->height + rootbr->kinp->height); if (aveh < minh + MINARC) aveh = minh + MINARC; hroot = aveh; maxhroot = RMHROOT*hroot; /* maximal possible hroot */ len = (hroot - rootbr->height) + (hroot - rootbr->kinp->height); rootbr->lengthc = len; rootbr->kinp->lengthc = len; } /* initclock */ /* approximate likelihood under the constaining assumption of clocklike branch lengths (with root on edge e) */ double clock_alklhd(int e) { initclock(e); Ctree->lklhdc = treelkl(Ctree); return Ctree->lklhdc; } /* clock_alklhd */ /* log-likelihood given height ht at node pointed to by chep */ double heightlkl(double ht) { Node *rp; double len; /* adjust branch lengths */ chep->height = ht; /* descendent branches */ rp = chep; while (rp->isop != chep) { rp = rp->isop; len = chep->height - rp->kinp->height; rp->kinp->lengthc = len; rp->lengthc = len; } /* upward branch */ if (chep == rootbr || chep->kinp == rootbr) { len = (hroot - chep->height) + (hroot - chep->kinp->height); chep->lengthc = len; chep->kinp->lengthc = len; } else { rp = chep->kinp; while (rp->isop->height <= 0.0) rp = rp->isop; chep->lengthc = rp->isop->height - chep->height; chep->kinp->lengthc = rp->isop->height - chep->height; } /* compute likelihood */ Ctree->lklhdc = treelkl(Ctree); return -(Ctree->lklhdc); /* we use a minimizing procedure */ } /* heightlkl */ /* optimize current height */ void optheight(void) { double he, fx, f2x, minh, maxh, len; Node *rp; /* current height */ he = chep->height; /* minimum */ minh = 0.0; rp = chep; while (rp->isop != chep) { rp = rp->isop; if (rp->kinp->height > minh) minh = rp->kinp->height; } minh += MINARC; /* maximum */ if (chep == rootbr || chep->kinp == rootbr) { maxh = hroot; } else { rp = chep->kinp; while (rp->isop->height <= 0.0) rp = rp->isop; maxh = rp->isop->height; } maxh -= MINARC; /* check borders for height */ if (he < minh) he = minh; if (he > maxh) he = maxh; /* optimization */ if (!(he == minh && he == maxh)) he = onedimenmin(minh, he, maxh, heightlkl, EPSILON_HEIGHTS, &fx, &f2x); /* variance of height */ f2x = fabs(f2x); if (1.0/(maxhroot*maxhroot) < f2x) chep->varheight = 1.0/f2x; else chep->varheight = maxhroot*maxhroot; /* adjust branch lengths */ chep->height = he; /* descendent branches */ rp = chep; while (rp->isop != chep) { rp = rp->isop; len = chep->height - rp->kinp->height; rp->kinp->lengthc = len; rp->lengthc = len; } /* upward branch */ if (chep == rootbr || chep->kinp == rootbr) { len = (hroot - chep->height) + (hroot - chep->kinp->height); chep->lengthc = len; chep->kinp->lengthc = len; } else { rp = chep->kinp; while (rp->isop->height <= 0.0) rp = rp->isop; chep->lengthc = rp->isop->height - chep->height; chep->kinp->lengthc = rp->isop->height - chep->height; } } /* optheight */ /* log-likelihood given height ht at root */ double rheightlkl(double ht) { double len; /* adjust branch lengths */ hroot = ht; len = (hroot - rootbr->height) + (hroot - rootbr->kinp->height); rootbr->lengthc = len; rootbr->kinp->lengthc = len; /* compute likelihood */ Ctree->lklhdc = treelkl(Ctree); return -(Ctree->lklhdc); /* we use a minimizing procedure */ } /* rheightlkl */ /* optimize height of root */ void optrheight(void) { double he, fx, f2x, minh, len; /* current height */ he = hroot; /* minimum */ if (rootbr->height > rootbr->kinp->height) minh = rootbr->height; else minh = rootbr->kinp->height; minh += MINARC; /* check borders for height */ if (he < minh) he = minh; if (he > maxhroot) he = maxhroot; /* optimization */ he = onedimenmin(minh, he, maxhroot, rheightlkl, EPSILON_HEIGHTS, &fx, &f2x); /* variance of height of root */ f2x = fabs(f2x); if (1.0/(maxhroot*maxhroot) < f2x) varhroot = 1.0/f2x; else varhroot = maxhroot*maxhroot; /* adjust branch lengths */ hroot = he; len = (hroot - rootbr->height) + (hroot - rootbr->kinp->height); rootbr->lengthc = len; rootbr->kinp->lengthc = len; } /* optrheight */ /* exact likelihood under the constaining assumption of clocklike branch lengths (with root on edge e) */ double clock_lklhd(int e) { int h, nconv; double old; Numitc = 0; Convergc = FALSE; initclock(e); do { Numitc++; nconv = 0; /* optimize height of root */ old = hroot; optrheight(); if (fabs(old - hroot) < EPSILON_HEIGHTS) nconv++; /* optimize height of nodes */ for (h = Numhts-1; h >= 0; h--) { /* pointer chep to current height node */ chep = heights[h]; /* store old value */ old = chep->height; /* find better height */ optheight(); /* converged ? */ if (fabs(old - chep->height) < EPSILON_HEIGHTS) nconv++; } if (nconv == Numhts+1) Convergc = TRUE; } while (Numitc < MAXIT && !Convergc); /* compute final likelihood */ Ctree->lklhdc = treelkl(Ctree); return Ctree->lklhdc; } /* clock_lklhd */ /* find out the edge containing the root */ int findrootedge() { int e, ebest; double logbest, logtest; /* compute the likelihood for all edges and take the edge with best likelihood (using approximate ML) */ ebest = 0; logbest = clock_alklhd(0); numbestroot = 1; for (e = 1; e < Numspc+Numibrnch; e++) { logtest = clock_alklhd(e); if (logtest > logbest) { ebest = e; logbest = logtest; numbestroot = 1; } else if (logtest == logbest) { numbestroot++; } } return ebest; } /* findrootedge */ /* show heights and corresponding standard errors */ void resultheights(FILE *fp) { int h, num; Node *cp; fprintf(fp, " height S.E. of node common to branches\n"); for (h = 0; h < Numhts; h++) { fprintf(fp, "%.5f %.5f ", (heights[h]->height)*0.01, sqrt(heights[h]->varheight)*0.01); cp = heights[h]; do { num = (cp->number) + 1; if (cp->kinp->isop != NULL) num += Numspc; /* internal branch */ fprintf(fp, "%d ", num); cp = cp->isop; } while (cp != heights[h]); fprintf(fp, "\n"); } fprintf(fp, "%.5f %.5f of root at branch %d\n", hroot*0.01, sqrt(varhroot)*0.01, locroot+1); } /* resultheights */ tree-puzzle-5.2/src/sprng/0000777000076400001440000000000010075312110011321 5tree-puzzle-5.2/src/sprng/primelist-lcg64.h0000644000076400001440000060136207755105700014363 #define PRIMELISTSIZE1 1000 #define STEP 10000 #define PRIMELISTSIZE2 15613 unsigned int prime_list[PRIMELISTSIZE2] = { 3037000493U, 3037000453U, 3037000429U, 3037000427U, 3037000399U, 3037000391U, 3037000333U, 3037000331U, 3037000303U, 3037000289U, 3037000249U, 3037000193U, 3037000181U, 3037000177U, 3037000159U, 3037000121U, 3037000111U, 3037000103U, 3037000069U, 3037000039U, 3037000013U, 3036999991U, 3036999983U, 3036999941U, 3036999899U, 3036999887U, 3036999877U, 3036999841U, 3036999821U, 3036999817U, 3036999811U, 3036999803U, 3036999773U, 3036999769U, 3036999761U, 3036999739U, 3036999737U, 3036999733U, 3036999727U, 3036999499U, 3036999487U, 3036999473U, 3036999467U, 3036999457U, 3036999443U, 3036999439U, 3036999431U, 3036999403U, 3036999379U, 3036999341U, 3036999319U, 3036999307U, 3036999293U, 3036999283U, 3036999271U, 3036999233U, 3036999209U, 3036999167U, 3036999157U, 3036999137U, 3036999113U, 3036999101U, 3036999089U, 3036999079U, 3036999067U, 3036999061U, 3036999023U, 3036999019U, 3036999001U, 3036998999U, 3036998989U, 3036998977U, 3036998963U, 3036998957U, 3036998933U, 3036998903U, 3036998873U, 3036998857U, 3036998849U, 3036998843U, 3036998837U, 3036998803U, 3036998777U, 3036998761U, 3036998759U, 3036998743U, 3036998717U, 3036998611U, 3036998599U, 3036998567U, 3036998563U, 3036998561U, 3036998537U, 3036998477U, 3036998449U, 3036998429U, 3036998401U, 3036998381U, 3036998347U, 3036998333U, 3036998329U, 3036998299U, 3036998267U, 3036998257U, 3036998249U, 3036998231U, 3036998213U, 3036998183U, 3036998161U, 3036998113U, 3036998093U, 3036998071U, 3036998051U, 3036998047U, 3036998011U, 3036998009U, 3036997973U, 3036997939U, 3036997933U, 3036997897U, 3036997853U, 3036997837U, 3036997813U, 3036997811U, 3036997787U, 3036997783U, 3036997751U, 3036997741U, 3036997727U, 3036997721U, 3036997709U, 3036997697U, 3036997693U, 3036997643U, 3036997631U, 3036997619U, 3036997603U, 3036997597U, 3036997577U, 3036997559U, 3036997511U, 3036997501U, 3036997493U, 3036997393U, 3036997391U, 3036997343U, 3036997339U, 3036997331U, 3036997289U, 3036997279U, 3036997217U, 3036997213U, 3036997169U, 3036997151U, 3036997133U, 3036997109U, 3036997081U, 3036997063U, 3036997021U, 3036996983U, 3036996947U, 3036996931U, 3036996923U, 3036996901U, 3036996883U, 3036996863U, 3036996829U, 3036996817U, 3036996799U, 3036996769U, 3036996761U, 3036996737U, 3036996713U, 3036996709U, 3036996707U, 3036996673U, 3036996631U, 3036996601U, 3036996587U, 3036996553U, 3036996527U, 3036996497U, 3036996491U, 3036996481U, 3036996451U, 3036996439U, 3036996421U, 3036996379U, 3036996373U, 3036996353U, 3036996349U, 3036996329U, 3036996307U, 3036996299U, 3036996283U, 3036996253U, 3036996247U, 3036996211U, 3036996197U, 3036996121U, 3036996091U, 3036996077U, 3036996071U, 3036996049U, 3036996019U, 3036996013U, 3036995981U, 3036995977U, 3036995953U, 3036995933U, 3036995921U, 3036995909U, 3036995893U, 3036995887U, 3036995881U, 3036995867U, 3036995839U, 3036995833U, 3036995827U, 3036995791U, 3036995761U, 3036995737U, 3036995723U, 3036995711U, 3036995671U, 3036995641U, 3036995627U, 3036995609U, 3036995603U, 3036995581U, 3036995579U, 3036995573U, 3036995543U, 3036995531U, 3036995527U, 3036995491U, 3036995477U, 3036995459U, 3036995369U, 3036995281U, 3036995267U, 3036995257U, 3036995249U, 3036995239U, 3036995189U, 3036995161U, 3036995153U, 3036995123U, 3036995089U, 3036995083U, 3036995057U, 3036995051U, 3036995041U, 3036995021U, 3036994997U, 3036994963U, 3036994931U, 3036994921U, 3036994897U, 3036994889U, 3036994879U, 3036994847U, 3036994799U, 3036994787U, 3036994777U, 3036994747U, 3036994717U, 3036994703U, 3036994679U, 3036994673U, 3036994663U, 3036994661U, 3036994627U, 3036994621U, 3036994619U, 3036994591U, 3036994549U, 3036994547U, 3036994531U, 3036994511U, 3036994507U, 3036994489U, 3036994469U, 3036994439U, 3036994423U, 3036994417U, 3036994397U, 3036994381U, 3036994369U, 3036994349U, 3036994327U, 3036994309U, 3036994283U, 3036994249U, 3036994237U, 3036994229U, 3036994211U, 3036994193U, 3036994141U, 3036994099U, 3036994073U, 3036994069U, 3036994063U, 3036994043U, 3036994039U, 3036994033U, 3036994001U, 3036993977U, 3036993937U, 3036993913U, 3036993901U, 3036993893U, 3036993871U, 3036993769U, 3036993737U, 3036993727U, 3036993719U, 3036993677U, 3036993667U, 3036993613U, 3036993607U, 3036993601U, 3036993587U, 3036993571U, 3036993569U, 3036993541U, 3036993539U, 3036993529U, 3036993527U, 3036993511U, 3036993469U, 3036993437U, 3036993413U, 3036993367U, 3036993359U, 3036993331U, 3036993329U, 3036993319U, 3036993283U, 3036993277U, 3036993257U, 3036993251U, 3036993241U, 3036993233U, 3036993221U, 3036993217U, 3036993181U, 3036993161U, 3036993143U, 3036993133U, 3036993131U, 3036993107U, 3036993103U, 3036993097U, 3036993083U, 3036993077U, 3036993073U, 3036993023U, 3036992983U, 3036992977U, 3036992969U, 3036992957U, 3036992953U, 3036992921U, 3036992899U, 3036992879U, 3036992873U, 3036992869U, 3036992809U, 3036992773U, 3036992753U, 3036992747U, 3036992743U, 3036992741U, 3036992731U, 3036992719U, 3036992711U, 3036992701U, 3036992681U, 3036992669U, 3036992639U, 3036992579U, 3036992521U, 3036992507U, 3036992503U, 3036992461U, 3036992437U, 3036992423U, 3036992401U, 3036992383U, 3036992377U, 3036992341U, 3036992333U, 3036992293U, 3036992291U, 3036992249U, 3036992207U, 3036992191U, 3036992141U, 3036992131U, 3036992113U, 3036992087U, 3036992083U, 3036992069U, 3036992051U, 3036992033U, 3036992017U, 3036992011U, 3036991987U, 3036991981U, 3036991949U, 3036991943U, 3036991897U, 3036991891U, 3036991883U, 3036991861U, 3036991777U, 3036991757U, 3036991753U, 3036991747U, 3036991717U, 3036991649U, 3036991627U, 3036991619U, 3036991591U, 3036991543U, 3036991511U, 3036991501U, 3036991481U, 3036991453U, 3036991381U, 3036991361U, 3036991357U, 3036991327U, 3036991303U, 3036991301U, 3036991271U, 3036991261U, 3036991253U, 3036991249U, 3036991247U, 3036991189U, 3036991183U, 3036991171U, 3036991147U, 3036991127U, 3036991109U, 3036991081U, 3036991063U, 3036991049U, 3036991037U, 3036991033U, 3036991031U, 3036991021U, 3036990997U, 3036990977U, 3036990961U, 3036990949U, 3036990923U, 3036990907U, 3036990899U, 3036990893U, 3036990871U, 3036990851U, 3036990829U, 3036990779U, 3036990769U, 3036990763U, 3036990739U, 3036990727U, 3036990709U, 3036990703U, 3036990611U, 3036990559U, 3036990491U, 3036990431U, 3036990421U, 3036990401U, 3036990391U, 3036990379U, 3036990371U, 3036990323U, 3036990317U, 3036990277U, 3036990263U, 3036990247U, 3036990233U, 3036990227U, 3036990199U, 3036990193U, 3036990167U, 3036990163U, 3036990157U, 3036990071U, 3036990059U, 3036990049U, 3036990037U, 3036990029U, 3036990017U, 3036989999U, 3036989993U, 3036989983U, 3036989957U, 3036989863U, 3036989821U, 3036989797U, 3036989779U, 3036989723U, 3036989693U, 3036989687U, 3036989651U, 3036989611U, 3036989609U, 3036989603U, 3036989573U, 3036989561U, 3036989539U, 3036989477U, 3036989471U, 3036989441U, 3036989419U, 3036989381U, 3036989377U, 3036989363U, 3036989357U, 3036989353U, 3036989323U, 3036989297U, 3036989281U, 3036989261U, 3036989209U, 3036989167U, 3036989159U, 3036989149U, 3036989129U, 3036989107U, 3036989101U, 3036989077U, 3036989071U, 3036989063U, 3036989041U, 3036989027U, 3036988991U, 3036988879U, 3036988849U, 3036988819U, 3036988751U, 3036988739U, 3036988729U, 3036988727U, 3036988723U, 3036988699U, 3036988679U, 3036988673U, 3036988667U, 3036988651U, 3036988637U, 3036988631U, 3036988627U, 3036988583U, 3036988573U, 3036988571U, 3036988543U, 3036988523U, 3036988483U, 3036988469U, 3036988429U, 3036988417U, 3036988399U, 3036988397U, 3036988393U, 3036988387U, 3036988369U, 3036988349U, 3036988319U, 3036988313U, 3036988309U, 3036988301U, 3036988277U, 3036988271U, 3036988117U, 3036988111U, 3036988109U, 3036988081U, 3036988079U, 3036988043U, 3036988037U, 3036988027U, 3036988021U, 3036987991U, 3036987979U, 3036987937U, 3036987931U, 3036987929U, 3036987917U, 3036987913U, 3036987901U, 3036987883U, 3036987871U, 3036987809U, 3036987799U, 3036987773U, 3036987743U, 3036987731U, 3036987727U, 3036987719U, 3036987691U, 3036987659U, 3036987637U, 3036987631U, 3036987601U, 3036987589U, 3036987587U, 3036987581U, 3036987563U, 3036987557U, 3036987553U, 3036987533U, 3036987529U, 3036987523U, 3036987521U, 3036987469U, 3036987439U, 3036987427U, 3036987361U, 3036987337U, 3036987319U, 3036987311U, 3036987293U, 3036987251U, 3036987241U, 3036987197U, 3036987167U, 3036987127U, 3036987089U, 3036987077U, 3036987073U, 3036987067U, 3036987061U, 3036987043U, 3036986969U, 3036986957U, 3036986917U, 3036986881U, 3036986863U, 3036986851U, 3036986839U, 3036986803U, 3036986791U, 3036986789U, 3036986767U, 3036986759U, 3036986737U, 3036986713U, 3036986669U, 3036986609U, 3036986599U, 3036986593U, 3036986569U, 3036986509U, 3036986507U, 3036986501U, 3036986479U, 3036986441U, 3036986431U, 3036986417U, 3036986411U, 3036986383U, 3036986333U, 3036986287U, 3036986279U, 3036986203U, 3036986189U, 3036986167U, 3036986129U, 3036986123U, 3036986107U, 3036986041U, 3036986023U, 3036986009U, 3036985999U, 3036985993U, 3036985979U, 3036985949U, 3036985921U, 3036985877U, 3036985873U, 3036985837U, 3036985829U, 3036985817U, 3036985813U, 3036985799U, 3036985771U, 3036985753U, 3036985747U, 3036985741U, 3036985739U, 3036985733U, 3036985729U, 3036985709U, 3036985697U, 3036985673U, 3036985643U, 3036985613U, 3036985607U, 3036985603U, 3036985583U, 3036985561U, 3036985559U, 3036985547U, 3036985543U, 3036985499U, 3036985459U, 3036985439U, 3036985433U, 3036985409U, 3036985373U, 3036985361U, 3036985309U, 3036985291U, 3036985283U, 3036985267U, 3036985253U, 3036985249U, 3036985219U, 3036985207U, 3036985187U, 3036985177U, 3036985151U, 3036985097U, 3036985093U, 3036985073U, 3036985033U, 3036985031U, 3036985001U, 3036984997U, 3036984989U, 3036984971U, 3036984953U, 3036984943U, 3036984917U, 3036984887U, 3036984803U, 3036984799U, 3036984787U, 3036984773U, 3036984761U, 3036984751U, 3036984749U, 3036984721U, 3036984697U, 3036984673U, 3036984667U, 3036984637U, 3036984623U, 3036984589U, 3036984569U, 3036984563U, 3036984539U, 3036984527U, 3036984481U, 3036984479U, 3036984427U, 3036984421U, 3036984413U, 3036984407U, 3036984403U, 3036984373U, 3036984367U, 3036984361U, 3036984343U, 3036984319U, 3036984287U, 3036984259U, 3036984257U, 3036984253U, 3036984199U, 3036984191U, 3036984151U, 3036984133U, 3036984131U, 3036984089U, 3036984059U, 3036984053U, 3036984047U, 3036984017U, 3036983933U, 3036983923U, 3036983909U, 3036983897U, 3036983867U, 3036983843U, 3036983837U, 3036983827U, 3036983813U, 3036983809U, 3036983777U, 3036983771U, 3036983699U, 3036983689U, 3036983671U, 3036983657U, 3036983629U, 3036983623U, 3036983597U, 3036983567U, 3036983561U, 3036983539U, 3036983533U, 3036983497U, 3036983483U, 3036983441U, 3036983407U, 3036983387U, 3036983297U, 3036983281U, 3036983249U, 3036983203U, 3036983189U, 3036983177U, 3036983167U, 3036983137U, 3036983111U, 3036983099U, 3036983083U, 3036983063U, 3036983057U, 3036983041U, 3036982981U, 3036982937U, 3036982919U, 3036982853U, 3036982843U, 3036982841U, 3036982789U, 3036982777U, 3036982757U, 3036982727U, 3036982693U, 3036982643U, 3036982639U, 3036982601U, 3036982589U, 3036982577U, 3036982567U, 3036982547U, 3036982541U, 3036982523U, 3036982519U, 3036982489U, 3036982469U, 3036982451U, 3036982423U, 3036982397U, 3036982387U, 3036982349U, 3036982337U, 3036982331U, 3036982313U, 3036982297U, 3036982279U, 3036982271U, 3036982189U, 3036982139U, 3036982133U, 3036982121U, 3036982111U, 3036982103U, 3036982099U, 3036982093U, 3036982061U, 3036982043U, 3036982009U, 3036982001U, 3036981979U, 3036981967U, 3036981953U, 3036981931U, 3036981923U, 3036981917U, 3036981863U, 3036981859U, 3036981853U, 3036981851U, 3036981821U, 3036981811U, 3036981797U, 3036981763U, 3036981733U, 3036981713U, 3036981691U, 3036981659U, 3036981553U, 3036981547U, 3036981539U, 3036981533U, 3036981481U, 3036981421U, 3036981407U, 3036981401U, 3036981383U, 3036981373U, 3036981359U, 3036981347U, 3036981323U, 3036981313U, 3036981307U, 3036981301U, 3036981289U, 3036981287U, 3036981209U, 3036981179U, 3036981139U, 3036981097U, 3036981067U, 3036981043U, 3036981041U, 3036981023U, 3036981011U, 3036980971U, 3036980941U, 3036980917U, 3036980911U, 3036980897U, 3036980867U, 3036980851U, 3036980819U, 3036980803U, 3036980761U, 3036980753U, 3036980747U, 3036980701U, 3036980699U, 3036980677U, 3036980599U, 3036980579U, 3036980549U, 3036980537U, 3036980533U, 3036980519U, 3036980497U, 3036980491U, 3036980459U, 3036980423U, 3036980371U, 3036980363U, 3036980339U, 3036980327U, 3036980269U, 3036980267U, 3036980263U, 3036980207U, 3036980161U, 3036980129U, 3036980123U, 3036980117U, 3036980077U, 3036980071U, 3036980047U, 3036980041U, 3036980039U, 3036980033U, 3036980027U, 3036979997U, 3036979987U, 3036979937U, 3036979927U, 3036979919U, 3036979873U, 3036979861U, 3036979849U, 3036979837U, 3036979793U, 3036979787U, 3036979769U, 3036979763U, 3036979723U, 3036979709U, 3036979679U, 3036979661U, 3036979601U, 3036979597U, 3036979579U, 3036979571U, 3036979531U, 3036979529U, 3036979523U, 3036979457U, 3036979391U, 3036979357U, 3036979343U, 3036979339U, 3036979303U, 3036979301U, 3036979291U, 3036979289U, 3036979261U, 3036979249U, 3036979237U, 3036979223U, 3036762997U, 3036545581U, 3036327389U, 3036107951U, 3035888633U, 3035669363U, 3035449477U, 3035232667U, 3035014193U, 3034795427U, 3034577531U, 3034357853U, 3034138969U, 3033923621U, 3033706409U, 3033488597U, 3033267889U, 3033049871U, 3032832493U, 3032615063U, 3032396527U, 3032177359U, 3031960339U, 3031742731U, 3031526081U, 3031308359U, 3031092199U, 3030873071U, 3030655757U, 3030437257U, 3030218647U, 3029999191U, 3029780833U, 3029559389U, 3029339741U, 3029122153U, 3028904231U, 3028687897U, 3028467803U, 3028251181U, 3028034189U, 3027815579U, 3027597247U, 3027377317U, 3027158237U, 3026939441U, 3026721421U, 3026502179U, 3026282261U, 3026065561U, 3025847507U, 3025627663U, 3025409689U, 3025190813U, 3024971231U, 3024753383U, 3024533179U, 3024312673U, 3024094123U, 3023876753U, 3023655737U, 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104271161U, 104088581U, 103905899U, 103720889U, 103535363U, 103351607U, 103166803U, 102982193U, 102797509U, 102611801U, 102428533U, 102245177U, 102061153U, 101878417U, 101693441U, 101508191U, 101324557U, 101140019U, 100957291U, 100772813U, 100587523U, 100402817U, 100217561U, 100034317U, 99851249U, 99665549U, 99482633U, 99298943U, 99112829U, 98929081U, 98743261U, 98558099U, 98374879U, 98191759U, 98006033U, 97821839U, 97638559U, 97456841U, 97272631U, 97087433U, 96904513U, 96719809U, 96537893U, 96353401U, 96168011U, 95983787U, 95801747U, 95616853U, 95433263U, 95249807U, 95066039U, 94883111U, 94700833U, 94516717U, 94333933U, 94149721U, 93966659U, 93784181U, 93599687U, 93415661U, 93232427U, 93049301U, 92863711U, 92681111U, 92497303U, 92313943U, 92129753U, 91947211U, 91761893U, 91580219U, 91395749U, 91213127U, 91030321U, 90846887U, 90664879U, 90480161U, 90297667U, 90115583U, 89933297U, 89749379U, 89564353U, 89380243U, 89196911U, 89014231U, 88831753U, 88648711U, 88464433U, 88281301U, 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71540317U, 71360867U, 71180273U, 70999073U, 70818323U, 70636019U, 70455323U, 70275589U, 70095271U, 69913423U, 69732599U, 69552737U, 69373621U, 69192857U, 69011251U, 68831857U, 68650541U, 68469409U, 68288557U, 68108351U, 67927511U, 67746827U, 67567627U, 67387867U, 67208347U, 67028069U, 66848311U, 66666751U, 66487507U, 66307727U, 66128837U, 65950439U, 65770451U, 65589409U, 65410649U, 65230259U, 65049041U, 64870343U, 64688747U, 64507787U, 64327903U, 64147561U, 63968063U, 63789757U, 63610199U, 63430931U, 63251467U, 63071809U, 62892839U, 62713073U, 62532517U, 62352571U, 62173597U, 61994887U, 61815977U, 61636231U, 61456183U, 61275419U, 61094951U, 60915853U, 60737837U, 60559241U, 60379751U, 60201523U, 60021539U, 59841973U, 59663497U, 59484767U, 59305187U, 59125333U, 58945219U, 58767607U, 58589033U, 58410523U, 58231967U, 58052879U, 57873817U, 57694499U, 57514829U, 57335981U, 57158411U, 56980423U, 56800753U, 56624527U, 56446043U, 56266219U, 56088649U, 55910791U, 55732351U, 55555231U, 55376369U, 55197721U, 55019897U, 54841331U, 54662059U, 54485107U, 54306403U, 54126781U, 53949167U, 53770853U, 53593171U, 53413639U, 53235829U, 53058007U, 52880033U, 52702613U, 52525171U, 52347107U, 52168973U, 51990767U, 51813187U, 51636499U, 51458861U, 51281453U, 51104257U, 50925361U, 50748149U, 50570687U, 50394067U, 50216953U, 50039263U, 49861883U, 49684643U, 49508111U, 49332421U, 49155797U, 48978451U, 48802009U, 48623479U, 48446927U, 48269713U, 48092383U, 47913799U, 47737211U, 47559517U, 47382877U, 47205551U, 47028899U, 46852483U, 46675831U, 46499939U, 46323493U, 46146389U, 45969251U, 45792757U, 45616187U, 45441163U, 45266317U, 45089893U, 44914523U, 44738009U, 44563219U, 44387113U, 44210707U, 44034449U, 43858921U, 43682351U, 43505453U, 43330681U, 43154911U, 42978773U, 42801313U, 42625673U, 42449963U, 42274433U, 42100169U, 41923451U, 41748299U, 41572033U, 41396093U, 41219881U, 41044891U, 40868299U, 40695289U, 40518707U, 40343419U, 40168781U, 39994211U, 39817907U, 39642653U, 39468991U, 39294637U, 39120883U, 38945273U, 38772131U, 38597917U, 38422801U, 38249219U, 38075273U, 37901167U, 37725713U, 37551001U, 37377479U, 37201921U, 37029367U, 36854551U, 36679801U, 36505093U, 36330773U, 36157423U, 35984339U, 35809141U, 35635627U, 35461177U, 35287939U, 35114207U, 34939903U, 34767391U, 34591933U, 34418939U, 34244071U, 34069129U, 33893689U, 33721511U, 33548077U, 33374401U, 33202313U, 33028577U, 32856277U, 32682743U, 32509907U, 32337311U, 32163991U, 31991731U, 31819127U, 31646471U, 31473479U, 31300459U, 31127519U, 30953453U, 30781319U, 30609311U, 30437177U, 30265159U, 30092813U, 29922733U, 29750759U, 29579519U, 29406439U, 29235953U, 29062879U, 28890787U, 28718537U, 28546591U, 28374859U, 28204291U, 28031611U, 27861667U, 27689833U, 27518653U, 27347557U, 27174779U, 27004343U, 26834293U, 26662327U, 26491921U, 26321989U, 26150171U, 25979521U, 25809083U, 25638607U, 25468039U, 25298069U, 25124909U, 24955681U, 24783713U, 24614839U, 24444313U, 24274847U, 24105251U, 23935453U, 23765431U, 23595163U, 23425559U, 23256053U, 23085833U, 22916461U, 22747187U, 22578419U, 22409393U, 22239713U, 22068143U, 21900377U, 21731779U, 21563219U, 21394229U, 21226157U, 21056153U, 20887649U, 20718781U, 20551697U, 20382253U, 20213983U, 20045197U, 19878041U, 19710289U, 19541903U, 19374079U, 19206023U, 19038311U, 18870161U, 18703387U, 18536303U, 18368221U, 18201941U, 18033391U, 17866619U, 17699107U, 17532169U, 17366749U, 17201039U, 17032781U, 16867867U, 16702099U, 16535639U, 16369853U, 16203367U, 16036523U, 15870383U, 15705071U, 15539987U, 15374041U, 15208997U, 15042919U, 14876951U, 14712427U, 14547283U, 14382007U, 14218571U, 14053619U, 13887953U, 13724233U, 13560847U, 13395559U, 13231343U, 13067423U, 12902137U, 12738433U, 12575881U, 12411409U, 12249493U, 12086059U, 11923057U, 11760059U, 11597701U, 11435887U, 11272697U, 11109827U, 10947941U, 10786267U, 10624787U, 10463443U, 10302407U, 10140307U, 9979111U, 9817057U, 9655759U, 9495601U, 9334487U, 9174793U, 9014101U, 8853359U, 8693653U, 8534489U, 8375273U, 8215633U, 8056423U, 7896949U, 7738559U, 7580459U, 7421383U, 7263143U, 7104341U, 6947753U, 6791437U, 6633877U, 6477301U, 6319483U, 6163567U, 6007247U, 5851717U, 5695831U, 5539363U, 5383601U, 5229331U, 5074633U, 4920613U, 4766999U, 4613237U, 4459951U, 4307453U, 4154791U, 4002547U, 3849943U, 3698881U, 3548471U, 3396661U, 3246119U, 3097141U, 2948161U, 2799451U, 2650931U, 2503597U, 2356573U, 2209499U, 2063573U, 1918439U, 1774937U, 1630987U, 1488133U, 1346567U, 1205653U, 1066909U, 927853U, 791447U, 656683U, 523417U, 393073U, 266083U, 143687U }; tree-puzzle-5.2/src/sprng/interface.h0000644000076400001440000000273107756425572013406 #ifndef _interface_h_ #define _interface_h_ #ifndef ANSI_ARGS #ifdef __STDC__ #define ANSI_ARGS(args) args #else #define ANSI_ARGS(args) () #endif #endif #ifdef __cplusplus extern "C" { #endif int get_rn_int ANSI_ARGS((int *igenptr)); float get_rn_flt ANSI_ARGS((int *igenptr)); double get_rn_dbl ANSI_ARGS((int *igenptr)); int *init_rng ANSI_ARGS(( int gennum, int total_gen, int seed, int mult)); int spawn_rng ANSI_ARGS((int *igenptr, int nspawned, int ***newgens, int checkid) ); int make_new_seed ANSI_ARGS((void)); int make_new_seed_mpi ANSI_ARGS((void)); int get_seed__rng ANSI_ARGS((int *genptr)); int free_rng ANSI_ARGS((int *genptr)); int pack_rng ANSI_ARGS(( int *genptr, char **buffer)); int *unpack_rng ANSI_ARGS(( char *packed)); int print_rng ANSI_ARGS(( int *igen)); int *checkID ANSI_ARGS(( int *igen)); int *addID ANSI_ARGS(( int *igen)); int *deleteID ANSI_ARGS(( int *igen)); /* HAS ;-) */ #if 0 int *init_rng_simple ANSI_ARGS(( int seed, int mult)); int *init_rng_simple_mpi ANSI_ARGS(( int seed, int mult)); int get_rn_int_simple ANSI_ARGS((void)); int get_rn_int_simple_mpi ANSI_ARGS((void)); float get_rn_flt_simple ANSI_ARGS((void)); float get_rn_flt_simple_mpi ANSI_ARGS((void)); double get_rn_dbl_simple ANSI_ARGS((void)); double get_rn_dbl_simple_mpi ANSI_ARGS((void)); int pack_rng_simple ANSI_ARGS((char **buffer)); int *unpack_rng_simple ANSI_ARGS(( char *packed)); int print_rng_simple ANSI_ARGS((void)); #endif #ifdef __cplusplus } #endif #endif tree-puzzle-5.2/src/sprng/primelist-lcg.h0000644000076400001440000004136507755105712014215 #define PRIMELISTSIZE1 1000 #define STEP 1000 #define PRIMELISTSIZE2 1778 int prime_list[PRIMELISTSIZE2] = { 11863279, 11863259, 11863253, 11863249, 11863237, 11863213, 11863207, 11863183, 11863171, 11863153, 11863151, 11863133, 11863121, 11863109, 11863099, 11863073, 11863067, 11863057, 11863039, 11863037, 11863031, 11863021, 11862989, 11862979, 11862959, 11862919, 11862911, 11862881, 11862869, 11862857, 11862839, 11862803, 11862791, 11862761, 11862713, 11862703, 11862701, 11862679, 11862673, 11862661, 11862623, 11862611, 11862581, 11862577, 11862569, 11862563, 11862547, 11862527, 11862493, 11862469, 11862439, 11862391, 11862373, 11862343, 11862317, 11862313, 11862307, 11862293, 11862271, 11862269, 11862259, 11862241, 11862239, 11862233, 11862229, 11862223, 11862217, 11862203, 11862199, 11862167, 11862157, 11862083, 11862049, 11862031, 11862029, 11862013, 11862007, 11861987, 11861959, 11861953, 11861921, 11861917, 11861887, 11861879, 11861873, 11861849, 11861827, 11861819, 11861803, 11861791, 11861749, 11861713, 11861711, 11861701, 11861693, 11861687, 11861683, 11861671, 11861659, 11861639, 11861627, 11861611, 11861599, 11861581, 11861579, 11861573, 11861569, 11861539, 11861527, 11861467, 11861441, 11861429, 11861413, 11861411, 11861407, 11861401, 11861371, 11861363, 11861357, 11861351, 11861327, 11861303, 11861299, 11861293, 11861273, 11861237, 11861231, 11861221, 11861219, 11861197, 11861191, 11861167, 11861159, 11861141, 11861131, 11861107, 11861099, 11861093, 11861089, 11861081, 11861071, 11861033, 11861011, 11860993, 11860973, 11860963, 11860897, 11860867, 11860859, 11860837, 11860811, 11860789, 11860787, 11860777, 11860753, 11860741, 11860727, 11860703, 11860699, 11860697, 11860691, 11860687, 11860669, 11860661, 11860649, 11860643, 11860637, 11860627, 11860619, 11860613, 11860573, 11860547, 11860517, 11860489, 11860487, 11860483, 11860477, 11860469, 11860411, 11860397, 11860379, 11860327, 11860267, 11860243, 11860231, 11860223, 11860207, 11860171, 11860151, 11860133, 11860109, 11860103, 11860097, 11860087, 11860081, 11860049, 11860039, 11860031, 11860021, 11859997, 11859989, 11859979, 11859961, 11859929, 11859923, 11859917, 11859907, 11859901, 11859893, 11859889, 11859877, 11859853, 11859847, 11859833, 11859821, 11859817, 11859791, 11859751, 11859739, 11859719, 11859713, 11859707, 11859643, 11859611, 11859583, 11859571, 11859569, 11859563, 11859541, 11859539, 11859509, 11859503, 11859487, 11859481, 11859473, 11859461, 11859457, 11859451, 11859433, 11859427, 11859383, 11859377, 11859371, 11859359, 11859349, 11859311, 11859307, 11859293, 11859269, 11859247, 11859241, 11859233, 11859187, 11859179, 11859167, 11859163, 11859157, 11859151, 11859139, 11859137, 11859109, 11859101, 11859083, 11859079, 11859077, 11859073, 11859061, 11859049, 11859031, 11859017, 11858989, 11858971, 11858969, 11858953, 11858947, 11858921, 11858897, 11858893, 11858851, 11858839, 11858813, 11858807, 11858801, 11858783, 11858779, 11858747, 11858729, 11858723, 11858719, 11858701, 11858683, 11858659, 11858657, 11858629, 11858599, 11858597, 11858579, 11858573, 11858569, 11858557, 11858551, 11858543, 11858533, 11858479, 11858447, 11858443, 11858423, 11858387, 11858381, 11858377, 11858359, 11858323, 11858311, 11858291, 11858281, 11858279, 11858269, 11858267, 11858243, 11858227, 11858201, 11858177, 11858159, 11858149, 11858131, 11858101, 11858059, 11858057, 11858051, 11858039, 11858029, 11858023, 11858017, 11857999, 11857991, 11857969, 11857931, 11857913, 11857907, 11857889, 11857883, 11857877, 11857873, 11857837, 11857831, 11857819, 11857817, 11857801, 11857793, 11857787, 11857777, 11857763, 11857759, 11857753, 11857751, 11857711, 11857709, 11857697, 11857693, 11857667, 11857661, 11857613, 11857591, 11857589, 11857543, 11857529, 11857523, 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567659, 554167, 540863, 527441, 514561, 501217, 488347, 475283, 462493, 449161, 435889, 423257, 410341, 397223, 384407, 371573, 358471, 345769, 333019, 320317, 307873, 295291, 282427, 269947, 257501, 245083, 232523, 220327, 208049, 195787, 183683, 171673, 159499, 147551, 135649, 123853, 112223, 100547, 89203, 77719, 66587, 55589, 44633, 34019, 23741, 13877, 4733 }; tree-puzzle-5.2/src/sprng/lcg.c0000644000076400001440000005276607756425660012221 /*************************************************************************/ /*************************************************************************/ /* Parallel 48 bit Linear Congruential Generator */ /* */ /* Author: Ashok Srinivasan, */ /* NCSA, University of Illinois, Urbana-Champaign */ /* E-Mail: ashoks@ncsa.uiuc.edu */ /* */ /* Disclaimer: NCSA expressly disclaims any and all warranties, expressed*/ /* or implied, concerning the enclosed software. The intent in sharing */ /* this software is to promote the productive interchange of ideas */ /* throughout the research community. All software is furnished on an */ /* "as is" basis. No further updates to this software should be */ /* expected. Although this may occur, no commitment exists. The authors */ /* certainly invite your comments as well as the reporting of any bugs. */ /* NCSA cannot commit that any or all bugs will be fixed. */ /*************************************************************************/ /*************************************************************************/ /* This is version 0.2, created 13 April 1998 */ #include #include #include #include "memory.h" #include "primes-lcg.h" #include "interface.h" #include #define NDEBUG #include #include "store.h" #define VERSION "00" #define GENTYPE VERSION "48 bit Linear Congruential Generator with Prime Addend" #if LONG_MAX > 2147483647L /* 32 bit integer */ #if LONG_MAX > 35184372088831L /* 46 bit integer */ #if LONG_MAX >= 9223372036854775807L /* 64 bit integer */ #define LONG_SPRNG #define LONG64 long #define store_long64 store_long #define store_long64array store_longarray #define load_long64 load_long #define load_long64array load_longarray #define INIT_SEED 0x2bc68cfe166dL #define MSB_SET 0x3ff0000000000000L #define LSB48 0xffffffffffffL #define AN1 0xdadf0ac00001L #define AN2 0xfefd7a400001L #define AN3 0x6417b5c00001L #define AN4 0xcf9f72c00001L #define AN5 0xbdf07b400001L #define AN6 0xf33747c00001L #define AN7 0xcbe632c00001L #define PMULT1 0xa42c22700000L #define PMULT2 0xfa858cb00000L #define PMULT3 0xd0c4ef00000L #define PMULT4 0xc3cc8e300000L #define PMULT5 0x11bdbe700000L #define PMULT6 0xb0f0e9f00000L #define PMULT7 0x6407de700000L #define MULT1 0x2875a2e7b175L /* 44485709377909 */ #define MULT2 0x5deece66dL /* 1575931494 */ #define MULT3 0x3eac44605265L /* 68909602460261 */ #define MULT4 0x275b38eb4bbdL /* 4327250451645 */ #define MULT5 0x1ee1429cc9f5L /* 33952834046453 */ #define MULT6 0x739a9cb08605L /* 127107890972165 */ #define MULT7 0x3228d7cc25f5L /* 55151000561141 */ #endif #endif #endif #if !defined(LONG_SPRNG) && defined(_LONG_LONG) #define LONG64 long long #define store_long64 store_longlong #define store_long64array store_longlongarray #define load_long64 load_longlong #define load_long64array load_longlongarray #define INIT_SEED 0x2bc68cfe166dLL #define MSB_SET 0x3ff0000000000000LL #define LSB48 0xffffffffffffLL #define AN1 0xdadf0ac00001LL #define AN2 0xfefd7a400001LL #define AN3 0x6417b5c00001LL #define AN4 0xcf9f72c00001LL #define AN5 0xbdf07b400001LL #define AN6 0xf33747c00001LL #define AN7 0xcbe632c00001LL #define PMULT1 0xa42c22700000LL #define PMULT2 0xfa858cb00000LL #define PMULT3 0xd0c4ef00000LL #define PMULT4 0x11bdbe700000LL #define PMULT5 0xc3cc8e300000LL #define PMULT6 0xb0f0e9f00000LL #define PMULT7 0x6407de700000LL #define MULT1 0x2875a2e7b175LL #define MULT2 0x5deece66dLL #define MULT3 0x3eac44605265LL #define MULT4 0x1ee1429cc9f5LL #define MULT5 0x275b38eb4bbdLL #define MULT6 0x739a9cb08605LL #define MULT7 0x3228d7cc25f5LL #endif #define TWO_M24 5.96046447753906234e-8 #define TWO_M48 3.5527136788005008323e-15 #include "multiply.h" #ifdef LittleEndian #define MSB 1 #else #define MSB 0 #endif #define LSB (1-MSB) #define LCGRUNUP 29 int MAX_STREAMS = 1<<19; #ifndef TOOMANY #define TOOMANY "generator has branched maximum number of times;\nindependence of streams cannot be guranteed\n" #endif #ifdef LONG64 struct rngen { unsigned LONG64 seed; int init_seed; int prime; int prime_position; int prime_next; char *gentype; int parameter; unsigned LONG64 multiplier; }; unsigned LONG64 mults[] = {MULT1,MULT2,MULT3,MULT4,MULT5,MULT6,MULT7}; unsigned LONG64 multiplier=0; #else struct rngen { int seed[2]; int init_seed; int prime; int prime_position; int prime_next; char *gentype; int parameter; int *multiplier; }; int mults[][4] = {{0x175,0xe7b,0x5a2,0x287},{0x66d,0xece,0x5de,0x000}, {0x265,0x605,0xc44,0x3ea},{0x9f5,0x9cc,0x142,0x1ee}, {0xbbd,0xeb4,0xb38,0x275},{0x605,0xb08,0xa9c,0x739}, {0x5f5,0xcc2,0x8d7,0x322}}; int *multiplier=NULL; #endif #define NPARAMS 7 int NGENS=0; void plus ANSI_ARGS((int *a, int *b, int *c)); void mult ANSI_ARGS((int *a, int *b, int *c, int size)); void advance_seed ANSI_ARGS((struct rngen *gen)); double get_rn_dbl ANSI_ARGS((int *gen)); #ifdef __STDC__ int bit_reverse(int n) #else int bit_reverse(n) int n; #endif { int i=31, rev=0; for(i=30; i>=0; i--) { rev |= (n&1)<>= 1; } return rev; } #ifdef __STDC__ void errprint(char *level, char *routine, char *error) #else void errprint(level, routine, error) char *level,*routine,*error; #endif { #ifdef CRAY #pragma _CRI guard 63 #endif fprintf(stderr,"%s from %s: %s\n",level,routine,error); #ifdef CRAY #pragma _CRI endguard 63 #endif } #ifdef __STDC__ int strxncmp(char *s1, char *s2, int n) #else int strxncmp(s1, s2, n) char *s1, *s2; int n; #endif { int i; for(i=0; i= MAX_STREAMS) /* check if gen_num is valid */ fprintf(stderr,"WARNING - init_rng: gennum: %d > maximum number of independent streams: %d\n\tIndependence of streams cannot be guranteed.\n", gennum, MAX_STREAMS); if (gennum < 0 || gennum >= total_gen) /* check if gen_num is valid */ { errprint("ERROR","init_rng","gennum out of range. "); return (int *) NULL; } seed &= 0x7fffffff; /* Only 31 LSB of seed considered */ if (mult < 0 || mult >= NPARAMS) { errprint("WARNING","init_rng","multiplier not valid. Using Default param"); mult = 0; } #ifdef LONG64 if(multiplier == 0) multiplier = mults[mult]; /* else if(multiplier != mults[mult]) fprintf(stderr,"WARNING: init_rng_d: Proposed multiplier does not agree with current multiplier.\n\t Independence of streams is not guaranteed\n");*/ #else if(multiplier == NULL) multiplier = mults[mult]; /*else if(strxncmp((char *) multiplier,(char *) mults[mult],4*sizeof(int)) != 0) fprintf(stderr,"WARNING: init_rng_d: Proposed multiplier does not agree with current multiplier.\n\t Independence of streams is not guaranteed\n");*/ #endif genptr = (struct rngen *) mymalloc(1*sizeof(struct rngen)); if(genptr == NULL) return NULL; genptr->gentype = GENTYPE; genptr->init_seed = seed; getprime(1, &(genptr->prime), gennum); genptr->prime_position = gennum; genptr->prime_next = total_gen; genptr->parameter = mult; #ifdef LONG64 genptr->seed = INIT_SEED; /* initialize generator */ genptr->seed ^= ((unsigned LONG64) seed)<<16; genptr->multiplier = mults[mult]; if (genptr->prime == 0) genptr->seed |= 1; #else genptr->seed[1] = 16651885^((seed<<16)&(0xff0000));/* initialize generator */ genptr->seed[0] = 2868876^((seed>>8)&(0xffffff)); genptr->multiplier = mults[mult]; if (genptr->prime == 0) genptr->seed[1] |= 1; #endif for(i=0; iprime_position); i++) get_rn_dbl( (int *) genptr); NGENS++; return (int *) genptr; } /* On machines with 32 bit integers, */ /* the Cray's 48 bit integer math is duplicated by breaking the problem into*/ /* steps. The algorithm is linear congruential. M is the multiplier and S*/ /* is the current seed. The 31 High order bits out of the 48 bits are returned*/ #ifdef __STDC__ int get_rn_int(int *igenptr) #else int get_rn_int(igenptr) int *igenptr; #endif { struct rngen *genptr = (struct rngen *) igenptr; #ifdef LONG64 multiply(genptr); return ((unsigned LONG64) genptr->seed) >> 17; #else int s[4], res[4]; multiply(genptr,genptr->multiplier,s,res); return (genptr->seed[0]<<7) | ((unsigned int) genptr->seed[1] >> 17) ; #endif } #ifdef __STDC__ float get_rn_flt(int *igenptr) #else float get_rn_flt(igenptr) int *igenptr; #endif { return (float) get_rn_dbl(igenptr); } /* get_rn_float */ #ifdef __STDC__ double get_rn_dbl(int *igenptr) #else double get_rn_dbl(igenptr) int *igenptr; #endif { struct rngen *genptr = (struct rngen *) igenptr; #ifdef LONG64 double temp[1]; unsigned LONG64 *ltemp; temp[0] = 0.0; multiply(genptr); /* Add defined(O2K) || defined(SGI) if optimization level is -O2 or lower */ #if defined(CONVEX) || defined(GENERIC) ltemp = (unsigned LONG64 *) temp; *ltemp = (genptr->seed<<4) | MSB_SET; return temp[0] - (double) 1.0; #else return genptr->seed*3.5527136788005008e-15; #endif #else static double equiv[1]; #define iran ((int *)equiv) #define ran (equiv) int expo, s[4], res[4]; multiply(genptr,genptr->multiplier,s,res); #if defined(HP) || defined(SUN) || defined(SOLARIS) || defined(GENERIC) expo = 1072693248; /*IEEE mantissa is 52 bits. We have only 48 bits, so we shift our result 4*/ /* bits left. 32-(24+4) = 4 bits are still blank in the lower word, so we*/ /* grab the low 4 bits of seedhi to fill these. */ iran[LSB] = genptr->seed[1] << 4 | genptr->seed[0] << 28; /* place the remaining (24-4)=20 bits of seedhi in bits 20-0 of ran. */ /* Expo occupies bits 30-20. Bit 31 (sign) is always zero. */ iran[MSB] = expo | genptr->seed[0] >> 4; return (*ran - (double) 1.0); #else return genptr->seed[0]*TWO_M24 + genptr->seed[1]*TWO_M48; #endif #undef ran #undef iran #endif } /* get_rn_dbl */ /*************************************************************************/ /*************************************************************************/ /* SPAWN_RNG: spawns new generators */ /*************************************************************************/ /*************************************************************************/ #ifdef __STDC__ int spawn_rng(int *igenptr, int nspawned, int ***newgens, int checkid) #else int spawn_rng(igenptr,nspawned, newgens, checkid) int *igenptr,nspawned, ***newgens, checkid; #endif { struct rngen **genptr, *tempptr = (struct rngen *) igenptr; int i, j; if (nspawned <= 0) /* check if nspawned is valid */ { nspawned = 1; errprint("WARNING","spawn_rng","nspawned <= 0. Default value of 1 used for nspawned"); } genptr = (struct rngen **) mymalloc(nspawned*sizeof(struct rngen *)); if(genptr == NULL) { *newgens = NULL; return 0; } for(i=0; iinit_seed = tempptr->init_seed; genptr[i]->prime_position = tempptr->prime_position + tempptr->prime_next*(i+1); if(genptr[i]->prime_position > MAXPRIMEOFFSET) { fprintf(stderr,"WARNING - spawn_rng: gennum: %d > maximum number of independent streams: %d\n\tIndependence of streams cannot be guranteed.\n", genptr[i]->prime_position, MAX_STREAMS); genptr[i]->prime_position %= MAXPRIMEOFFSET; } genptr[i]->prime_next = (nspawned+1)*tempptr->prime_next; getprime(1, &(genptr[i]->prime), genptr[i]->prime_position); genptr[i]->multiplier = tempptr->multiplier; genptr[i]->parameter = tempptr->parameter; genptr[i]->gentype = tempptr->gentype; #ifdef LONG64 genptr[i]->seed = INIT_SEED; /* initialize generator */ genptr[i]->seed ^= ((unsigned LONG64) tempptr->init_seed)<<16; if (genptr[i]->prime == 0) genptr[i]->seed |= 1; #else genptr[i]->seed[1] = 16651885^((tempptr->init_seed<<16)&(0xff0000)); genptr[i]->seed[0] = 2868876^((tempptr->init_seed>>8)&(0xffffff)); if (genptr[i]->prime == 0) genptr[i]->seed[1] |= 1; #endif if(genptr[i]->prime_position > MAXPRIMEOFFSET) advance_seed(genptr[i]); /* advance lcg 10^6 steps from initial seed */ for(j=0; jprime_position); j++) get_rn_dbl( (int *) genptr[i]); } tempptr->prime_next = (nspawned+1)*tempptr->prime_next; NGENS += nspawned; *newgens = (int **) genptr; if(checkid != 0) for(i=0; i>12; temp[i-1] &= 4095; } for(i=0; i<4 ; i++) result[i] = temp[i]; } /*multiply two 4 digit numbers in base 2^12 and return 'size' lowest order */ /* digits*/ #ifdef __STDC__ void mult(int *a, int *b, int *c, int size) #else void mult(a,b,c,size) int *a, *b, *c, size; #endif { int temp[8]; int i, j; for(i=0; i<8; i++) temp[i] = 0; for(i=0; i<4; i++) for(j=0; j<4; j++) temp[i+j] += a[i]*b[j]; for(i=1; i<8; i++) { temp[i] += temp[i-1]>>12; temp[i-1] &= 4095; } for(i=0; imultiplier == mults[i]) { found = 1; break; } if(found == 0) { fprintf(stderr,"WARNING: advance_seed: multiplier not acceptable.\n"); return ; } /* a^n, n = 10^6 and pmult = (a^n-1)/(a-1), n = 10^6 */ switch(i) { case 0 : an = AN1; pmult = PMULT1; break; case 1 : an = AN2; pmult = PMULT2; break; case 2 : an = AN3; pmult = PMULT3; break; case 3 : an = AN4; pmult = PMULT4; break; case 4 : an = AN5; pmult = PMULT5; break; case 5 : an = AN6; pmult = PMULT6; break; case 6 : an = AN7; pmult = PMULT7; break; default: fprintf(stderr,"WARNING: advance_seed parameters for multiplier %d not available\n", i); return; } gen->seed = gen->seed*an + pmult*gen->prime; gen->seed &= LSB48; #else int an[4], pmult[4], x0, x1, temp[4],temp2[4], i, found; for(i=0, found=0; imultiplier, (char *) (mults[i]), 4*sizeof(int)) == 0) { found = 1; break; } if(found == 0) { fprintf(stderr,"WARNING: advance_seed: multiplier not acceptable.\n"); return ; } /* a^n, n = 10^6 and pmult = (a^n-1)/(a-1), n = 10^6 */ switch(i) { case 0 : an[0] = 0x001; an[1] = 0xc00; an[2] = 0xf0a; an[3] = 0xdad; pmult[0] = 0x000; pmult[1] = 0x700; pmult[2] = 0xc22; pmult[3] = 0xa42; break; case 1 : an[0] = 0x001; an[1] = 0x400; an[2] = 0xd7a; an[3] = 0xfef; pmult[0] = 0x000; pmult[1] = 0xb00; pmult[2] = 0x58c; pmult[3] = 0xfa8; break; case 2 : an[0] = 0x001; an[1] = 0xc00; an[2] = 0x7b5; an[3] = 0x641; pmult[0] = 0x000; pmult[1] = 0xf00; pmult[2] = 0xc4e; pmult[3] = 0x0d0; break; case 3 : an[0] = 0x001; an[1] = 0xc00; an[2] = 0xf72; an[3] = 0xcf9; pmult[0] = 0x000; pmult[1] = 0x700; pmult[2] = 0xdbe; pmult[3] = 0x11b; break; case 4 : an[0] = 0x001; an[1] = 0x400; an[2] = 0x07b; an[3] = 0xbdf; pmult[0] = 0x000; pmult[1] = 0x300; pmult[2] = 0xc8e; pmult[3] = 0xc3c; break; case 5 : an[0] = 0x001; an[1] = 0xc00; an[2] = 0x747; an[3] = 0xf33; pmult[0] = 0x000; pmult[1] = 0xf00; pmult[2] = 0x0e9; pmult[3] = 0xb0f; break; case 6 : an[0] = 0x001; an[1] = 0xc00; an[2] = 0x632; an[3] = 0xcbe; pmult[0] = 0x000; pmult[1] = 0x700; pmult[2] = 0x7de; pmult[3] = 0x640; break; default: fprintf(stderr,"WARNING: advance_seed parameters for multiplier %d not available\n", i); return; } x0 = gen->seed[0]; x1 = gen->seed[1]; temp[0] = x1&4095; temp[1] = (x1>>12)&4095; temp[2] = x0&4095; /* seed */ temp[3] = (x0>>12)&4095; temp2[0] = gen->prime%(1<<12); temp2[1] = (gen->prime>>12)%(1<<12); temp2[2] = (gen->prime>>24)%(1<<12); temp2[3] = 0; /* prime */ mult(temp,an,temp,4); mult(temp2,pmult,temp2,4); plus(temp,temp2,temp); gen->seed[1] = (temp[1]<<12) + temp[0]; gen->seed[0] = (temp[3]<<12) + temp[2]; #endif } #ifdef __STDC__ int free_rng(int *genptr) #else int free_rng(genptr) int *genptr; #endif { struct rngen *q; q = (struct rngen *) genptr; free(q); NGENS--; return NGENS; } #ifdef __STDC__ int pack_rng( int *genptr, char **buffer) #else int pack_rng(genptr,buffer) int *genptr; char **buffer; #endif { unsigned char *p, *initp; unsigned int size, m[2], i; struct rngen *q; q = (struct rngen *) genptr; size = 5*4 /*sizeof(int)*/ + 2*8/*sizeof(unsigned LONG64)*/ + strlen(q->gentype)+1; /* The new load/store routines make using sizeof unnecessary. Infact, */ /* using sizeof could be erroneous. */ initp = p = (unsigned char *) mymalloc(size); if(p == NULL) { *buffer = NULL; return 0; } strcpy((char *)p,q->gentype); p += strlen(q->gentype)+1; #ifdef LONG64 p += store_long64(q->seed,8,p); p += store_int(q->init_seed,4,p); p += store_int(q->prime,4,p); p += store_int(q->prime_position,4,p); p += store_int(q->prime_next,4,p); p += store_int(q->parameter,4,p); p += store_long64(q->multiplier,8,p); #else m[0] = q->seed[0]>>8;m[1] = q->seed[0]<<24 | q->seed[1]; p += store_intarray(m,2,4,p); p += store_int(q->init_seed,4,p); p += store_int(q->prime,4,p); p += store_int(q->prime_position,4,p); p += store_int(q->prime_next,4,p); p += store_int(q->parameter,4,p); /* The following is done since the multiplier is stored in */ /* pieces of 12 bits each */ m[1] = q->multiplier[2]&0xff; m[1] <<= 24; m[1] |= q->multiplier[1]<<12; m[1] |= q->multiplier[0]; m[0] = (q->multiplier[3]<<4) | (q->multiplier[2]>>8); p += store_intarray(m,2,4,p); #endif *buffer = (char *) initp; assert(p-initp == size); return p-initp; } #ifdef __STDC__ int get_seed_rng(int *gen) #else int get_seed_rng(gen) int *gen; #endif { return ((struct rngen *) gen)->init_seed; } #ifdef __STDC__ int *unpack_rng( char *packed) #else int *unpack_rng(packed) char *packed; #endif { struct rngen *q; unsigned char *p; unsigned int m[4], m2[2], i; p = (unsigned char *) packed; q = (struct rngen *) mymalloc(sizeof(struct rngen)); if(q == NULL) return NULL; if(strcmp((char *)p,GENTYPE) != 0) { fprintf(stderr,"ERROR: Unpacked ' %.24s ' instead of ' %s '\n", p, GENTYPE); return NULL; } else q->gentype = GENTYPE; p += strlen(q->gentype)+1; #ifdef LONG64 p += load_long64(p,8,&q->seed); p += load_int(p,4,(unsigned int *)&q->init_seed); p += load_int(p,4,(unsigned int *)&q->prime); p += load_int(p,4,(unsigned int *)&q->prime_position); p += load_int(p,4,(unsigned int *)&q->prime_next); p += load_int(p,4,(unsigned int *)&q->parameter); p += load_long64(p,8,&q->multiplier); #else p += load_intarray(p,2,4,m2); q->seed[1] = m2[1]&0xffffff; q->seed[0] = m2[1]>>24 | m2[0]<<8; p += load_int(p,4,(unsigned int *)&q->init_seed); p += load_int(p,4,(unsigned int *)&q->prime); p += load_int(p,4,(unsigned int *)&q->prime_position); p += load_int(p,4,(unsigned int *)&q->prime_next); p += load_int(p,4,(unsigned int *)&q->parameter); p += load_intarray(p,2,4,m2); /* The following is done since the multiplier is stored in */ /* pieces of 12 bits each */ m[0] = m2[1]&0xfff; m[1] = (m2[1]&0xfff000)>>12; m[2] = (m2[1]&0xff000000)>>24 | (m2[0]&0xf)<<8; m[3] = (m2[0]&0xfff0)>>4; #endif if(q->parameter < 0 || q->parameter >= NPARAMS) { fprintf(stderr,"ERROR: Unpacked parameters not acceptable.\n"); free(q); return NULL; } q->multiplier = mults[q->parameter]; NGENS++; return (int *) q; } #ifdef __STDC__ int print_rng( int *igen) #else int print_rng(igen) int *igen; #endif { struct rngen *gen; printf("\n%s\n", GENTYPE+2); gen = (struct rngen *) igen; printf("\n \tseed = %d, stream_number = %d\tparameter = %d\n\n", gen->init_seed, gen->prime_position, gen->parameter); return 1; } /* HAS ;-) */ #if 0 #include "simple_.h" #include "../fwrap_.h" #endif tree-puzzle-5.2/src/sprng/lfg.c0000644000076400001440000007444607756425676012232 /*************************************************************************/ /*************************************************************************/ /* Parallel Modified Additive Lagged Fibonacci Generator */ /* */ /* Modified by: Ashok Srinivasan, */ /* NCSA, University of Illinois, Urbana-Champaign */ /* E-Mail: ashoks@ncsa.uiuc.edu */ /* */ /* Based on the Implementation by: */ /* Steven A. Cuccaro and Daniel V. Pryor, */ /* IDA/Center for Computing Sciences (CCS) */ /* E-Mail: cuccaro@super.org pryor@super.org */ /* */ /* Copyright 1996 September 3, United States Government as Represented */ /* by the Director, National Security Agency. All rights reserved. */ /* */ /* Disclaimer 1: NCSA expressly disclaims any and all warranties, expressed*/ /* or implied, concerning the enclosed software. The intent in sharing */ /* this software is to promote the productive interchange of ideas */ /* throughout the research community. All software is furnished on an */ /* "as is" basis. No further updates to this software should be */ /* expected. Although this may occur, no commitment exists. The authors */ /* certainly invite your comments as well as the reporting of any bugs. */ /* NCSA cannot commit that any or all bugs will be fixed. */ /* */ /* Disclaimer 2: CCS expressly disclaims any and all warranties, expressed */ /* or implied, concerning the enclosed software. This software was */ /* developed at CCS for use in internal research. The intent in sharing */ /* this software is to promote the productive interchange of ideas */ /* throughout the research community. All software is furnished on an */ /* "as is" basis. No further updates to this software should be */ /* expected. Although this may occur, no commitment exists. The authors */ /* certainly invite your comments as well as the reporting of any bugs. */ /* CCS cannot commit that any or all bugs will be fixed. */ /*************************************************************************/ /*************************************************************************/ /*************************************************************************/ /* This version has been modified to use two integer-based additive */ /* lagged-Fibonacci generators to produce integer, float and double */ /* values. The lagged-Fibonacci generators each have 31 bits of */ /* precision (after the bit fixed by the canonical form of the */ /* generator is removed), 31-bit values are generated by XORing */ /* the values after one has been shifted left one bit. The floating */ /* point value is formed by dividing the integer by 1.e+32 (the */ /* lsb's will be dropped from the mantissa to make room for the */ /* exponent), and two of these integer values in sequence are used */ /* to get the necessary precision for the double value. */ /* */ /* This method has the advantage that the generators pass fairly */ /* strict randomness tests, including the Birthday Spacings test */ /* that additive lagged-Fibonacci generators are well known to */ /* fail. The disadvantage is the additional time needed to do the */ /* division explicitly, which was avoided in previous versions. */ /* (As the division is by powers of 2, the user might well consider */ /* making machine-specific versions of this code to insert the bits */ /* into the appropriate places and avoid the problem entirely.) */ /*************************************************************************/ #include #include #include #include #include #define NDEBUG #include #include "interface.h" #include "memory.h" #include "store.h" /*#define PRINT_GEN*/ /* BITS_IN_INT_GEN is the log_2 of the modulus of the generator */ /* for portability this is set to 32, but can be modified; */ /* if modified, make sure INT_MOD_MASK can still be calculated */ #define BITS_IN_INT_GEN 32 /* INT_MOD_MASK is used to perform modular arithmetic - specifying */ /* this value compensates for different sized words on */ /* different architectures */ /* FLT_MULT is used in converting to float and double values; the */ /* odd form is due to a compiler glitch on our CM-5, which */ /* caused (0.5/(unsigned)(1<<31)) to be negative. */ #if (BITS_IN_INT_GEN==32) #define INT_MOD_MASK 0xffffffff #define FLT_MULT (0.25/(unsigned)(1<<30)) #else #define INT_MOD_MASK ((unsigned)(1<>1) /* MAX_BIT_INT is the largest bit position allowed in the index */ /* of the node - it equals BITS_IN_INT_GEN - 2 */ #define MAX_BIT_INT (BITS_IN_INT_GEN-2) /* INTX2_MASK is used in calculation of the node numbers */ #define INTX2_MASK ((1<=0;i--) { new_fill[0] = (new_fill[0]<<1) | (1&bitcnt(reg_fill[0]&temp)); new_fill[1] = (new_fill[1]<<1) | (1&bitcnt(reg_fill[1]&temp)); temp >>= 1; } for (i=28;i<32;i++) { temp = bitcnt(reg_fill[0]&(mask<>(32-i))); new_fill[0] |= (1&temp)<=0;i--) { if (b[i]&(1<hptr; int lval, kval; lval = ((struct rngen *)genptr)->lval; kval = ((struct rngen *)genptr)->kval; r0 = ((struct rngen *)genptr)->r0; r1 = ((struct rngen *)genptr)->r1; hptr = *hp; lptr = hptr + kval; if (lptr>=lval) lptr -= lval; /* INT_MOD_MASK causes arithmetic to be modular when integer size is */ /* different from generator modulus */ r0[hptr] = INT_MOD_MASK&(r0[hptr] + r0[lptr]); r1[hptr] = INT_MOD_MASK&(r1[hptr] + r1[lptr]); new_val = (r1[hptr]&(~1)) ^ (r0[hptr]>>1); if (--hptr < 0) hptr = lval - 1; /* skip an element in the sequence */ if (--lptr < 0) lptr = lval - 1; r0[hptr] = INT_MOD_MASK&(r0[hptr] + r0[lptr]); r1[hptr] = INT_MOD_MASK&(r1[hptr] + r1[lptr]); *hp = (--hptr < 0) ? lval-1 : hptr; return (new_val>>1); } #ifdef __STDC__ float get_rn_flt(int *genptr) #else float get_rn_flt(genptr) int *genptr; #endif /* returns value put into new position */ { unsigned long new_val; /* this cannot be unsigned int due to a bug in the SGI compiler */ unsigned *r0,*r1; int hptr,lptr,*hp = &((struct rngen *)genptr)->hptr; int lval, kval; lval = ((struct rngen *)genptr)->lval; kval = ((struct rngen *)genptr)->kval; r0 = ((struct rngen *)genptr)->r0; r1 = ((struct rngen *)genptr)->r1; hptr = *hp; lptr = hptr + kval; if (lptr>=lval) lptr -= lval; /* INT_MOD_MASK causes arithmetic to be modular when integer size is */ /* different from generator modulus */ r0[hptr] = INT_MOD_MASK&(r0[hptr] + r0[lptr]); r1[hptr] = INT_MOD_MASK&(r1[hptr] + r1[lptr]); new_val = (r1[hptr]&(~1)) ^ (r0[hptr]>>1); if (--hptr < 0) hptr = lval - 1; /* skip an element in the sequence */ if (--lptr < 0) lptr = lval - 1; r0[hptr] = INT_MOD_MASK&(r0[hptr] + r0[lptr]); r1[hptr] = INT_MOD_MASK&(r1[hptr] + r1[lptr]); *hp = (--hptr<0) ? lval-1 : hptr; return (new_val*FLT_MULT); } #ifdef __STDC__ double get_rn_dbl(int *genptr) #else double get_rn_dbl(genptr) int *genptr; #endif /* returns value put into new position */ { unsigned *r0,*r1; unsigned long temp1,temp2; /* Due to a bug in the SGI compiler, this should not be unsigned int */ int hptr,lptr,*hp = &((struct rngen *)genptr)->hptr; double new_val; int lval, kval; lval = ((struct rngen *)genptr)->lval; kval = ((struct rngen *)genptr)->kval; r0 = ((struct rngen *)genptr)->r0; r1 = ((struct rngen *)genptr)->r1; hptr = *hp; lptr = hptr + kval; if (lptr>=lval) lptr -= lval; /* INT_MOD_MASK causes arithmetic to be modular when integer size is */ /* different from generator modulus */ r0[hptr] = INT_MOD_MASK&(r0[hptr] + r0[lptr]); r1[hptr] = INT_MOD_MASK&(r1[hptr] + r1[lptr]); temp1 = (r1[hptr]&(~1)) ^ (r0[hptr]>>1); if (--hptr < 0) hptr = lval - 1; if (--lptr < 0) lptr = lval - 1; r0[hptr] = INT_MOD_MASK&(r0[hptr] + r0[lptr]); r1[hptr] = INT_MOD_MASK&(r1[hptr] + r1[lptr]); temp2 = (r1[hptr]&(~1)) ^ (r0[hptr]>>1); *hp = (--hptr < 0) ? lval-1 : hptr; new_val = ((unsigned int) temp2*(double)FLT_MULT + (unsigned int) temp1)*FLT_MULT; return (new_val); } /*************************************************************************/ /*************************************************************************/ /* INITIALIZE: starts the whole thing going */ /*************************************************************************/ /*************************************************************************/ #ifdef __STDC__ static int **initialize(int ngen, int param, unsigned seed, unsigned *nstart, unsigned initseed) #else static int **initialize(ngen,param, seed,nstart, initseed) int ngen, param; unsigned *nstart, seed, initseed; #endif { int i,j,k,l,*order, length; struct rngen **q; unsigned *nindex; length = valid[param].L; /* allocate memory for node number and fill of each generator */ order = (int *) mymalloc(ngen*sizeof(int)); q = (struct rngen **) mymalloc(ngen*sizeof(struct rngen *)); if (q == NULL || order == NULL) return NULL; for (i=0;ihptr = length - 1; q[i]->si = (unsigned *) mymalloc((length-1)*sizeof(unsigned)); q[i]->r0 = (unsigned *) mymalloc(length*sizeof(unsigned)); q[i]->r1 = (unsigned *) mymalloc(length*sizeof(unsigned)); q[i]->lval = length; q[i]->kval = valid[param].K; q[i]->param = param; q[i]->seed = seed; q[i]->init_seed = initseed; q[i]->gentype = GENTYPE; if (q[i]->r1 == NULL || q[i]->r0 == NULL || q[i]->si == NULL) return NULL; } /* specify register fills and node number arrays */ /* do fills in tree fashion so that all fills branch from index */ /* contained in nstart array */ q[0]->stream_number = nstart[0]; si_double(q[0]->si,nstart,length); get_fill(q[0]->si,q[0]->r0,param,seed); q[0]->si[0]++; get_fill(q[0]->si,q[0]->r1,param,seed); i = 1; order[0] = 0; if (ngen>1) while (1) { l = i; for (k=0;ksi; q[i]->stream_number = nindex[0]; si_double(nindex,nindex, length); for (j=0;jsi[j] = nindex[j]; get_fill(q[i]->si,q[i]->r0,param,seed); q[i]->si[0]++; get_fill(q[i]->si,q[i]->r1,param,seed); if (ngen == ++i) break; } if (ngen == i) break; for (k=l-1;k>0;k--) { order[2*k+1] = l+k; order[2*k] = order[k]; } order[1] = l; } free(order); for (i=ngen-1;i>=0;i--) { k = 0; for (j=1;jsi[j]) k = 1; if (!k) break; for (j=0;j=0) { for (j=0;j<4*length;j++) get_rn_int((int *)(q[i])); i--; } return((int **)q); } /*************************************************************************/ /*************************************************************************/ /* INIT_RNG's: user interface to start things off */ /*************************************************************************/ /*************************************************************************/ #ifdef __STDC__ int *init_rng( int gennum, int total_gen, int seed, int param) #else int *init_rng(gennum,total_gen,seed,param) int gennum,param,seed,total_gen; #endif { int doexit=0,i,k, length; int **p=NULL, *rng; unsigned *nstart=NULL,*si; /* gives back one generator (node gennum) with updated spawning */ /* info; should be called total_gen times, with different value */ /* of gennum in [0,total_gen) each call */ /* check values of gennum and total_gen */ if (total_gen <= 0) /* check if total_gen is valid */ { total_gen = 1; errprint("WARNING","init_rng","Total_gen <= 0. Default value of 1 used for total_gen"); } if (gennum >= MAX_STREAMS) /* check if gen_num is valid */ fprintf(stderr,"WARNING - init_rng: gennum: %d > maximum number of independent streams: %d\n\tIndependence of streams cannot be guranteed.\n", gennum, MAX_STREAMS); if (gennum < 0 || gennum >= total_gen) /* check if gen_num is valid */ { errprint("ERROR","init_rng","gennum out of range. "); return (int *) NULL; } seed &= 0x7fffffff; /* Only 31 LSB of seed considered */ if (param < 0 || param >= NPARAMS) { errprint("WARNING","init_rng","Parameter not valid. Using Default param"); param = 0; } /* check whether generators have previously been defined */ /* guard against access while defining generator parameters for */ /* the 1st time */ length = valid[param].L; /* determine parameters */ k = valid[param].K; if (!lval) { lval = length; /* determine parameters */ kval = k; gseed = seed^GS0; } else { if (lval != length) doexit++; if( seed != (gseed^GS0) ) doexit += 2; if (doexit) { if (doexit&1) errprint("WARNING","init_rng","changing global L value! Independence of streams is not guaranteed"); if (doexit&2) errprint("WARNING","init_rng","changing global seed value! Independence of streams is not guaranteed"); } } /* define the starting vector for the initial node */ nstart = (unsigned *) mymalloc((length-1)*sizeof(unsigned)); if (nstart == NULL) return NULL; nstart[0] = gennum; for (i=1;istream_number = gennum; /* update si array to allow for future spawning of generators */ si = ((struct rngen *)(p[0]))->si; while (si[0] < total_gen && !si[1]) si_double(si,si,length); NGENS++; free(nstart); rng = p[0]; free(p); return rng; } /*************************************************************************/ /*************************************************************************/ /* SPAWN_RNG: spawns new generators */ /*************************************************************************/ /*************************************************************************/ #ifdef __STDC__ int spawn_rng(int *genptr, int nspawned, int ***newgens, int checkid) #else int spawn_rng(genptr,nspawned,newgens, checkid) int *genptr,nspawned, ***newgens, checkid; #endif { int **q=NULL, i; unsigned *p; struct rngen *temp; if (nspawned <= 0) /* check if nspawned is valid */ { nspawned = 1; errprint("WARNING","spawn_rng","Nspawned <= 0. Default value of 1 used for nspawned"); } temp = (struct rngen *) genptr; p = temp->si; q = initialize(nspawned,temp->param,temp->seed,p,temp->init_seed); if (q == NULL) { *newgens = NULL; return 0; } si_double(p,p,temp->lval); NGENS += nspawned; *newgens = (int **) q; if(checkid != 0) for(i=0; ihptr); } #ifdef __STDC__ static int *get_fill_rng( int *genptr) #else static int *get_fill_rng(genptr) int *genptr; #endif { int i,*p; unsigned *pp; struct rngen *temp; temp = (struct rngen *) genptr; p = (int *) mymalloc(2*(temp->lval)*sizeof(int)); if(p == NULL) return NULL; pp = ((struct rngen *)genptr)->r0; for (i=0;ir1; for (i=0;ilval;i++) p[temp->lval+i] = pp[i]; return(p); } #ifdef __STDC__ static int *get_next_index_rng( int *genptr) #else static int *get_next_index_rng(genptr) int *genptr; #endif { int i,*p, lval; unsigned *pp; lval = ((struct rngen *) genptr)->lval; pp = ((struct rngen *)genptr)->si; p = (int *) mymalloc((lval-1)*sizeof(int)); if(p == NULL) return NULL; for (i=0;i>= 1; if (a[i+1]&1) a[i] ^= (1<>= 1; } #ifdef __STDC__ static int *get_node_index_rng( int *genptr) #else static int *get_node_index_rng(genptr) int *genptr; #endif { int *p, length; length = ( (struct rngen *) genptr)->lval; p = get_next_index_rng(genptr); if(p == NULL) return NULL; while (!(p[0]&1)) si_halve(p,length); si_halve(p, length); return(p); } /*************************************************************************/ /*************************************************************************/ /* MESSAGE PASSING ROUTINES */ /*************************************************************************/ /*************************************************************************/ #ifdef __STDC__ int pack_rng( int *genptr, char **buffer) #else int pack_rng(genptr,buffer) int *genptr; char **buffer; #endif { int i, size; struct rngen *q; unsigned char *p, *initp; q = (struct rngen *)genptr; size = (3*(q->lval)+5)*4 + strlen(q->gentype)+1; /* The new load/store routines make using sizeof unnecessary. Infact, */ /* using sizeof could be erroneous. */ initp = p = (unsigned char *) mymalloc(size); if(p == NULL) { *buffer = NULL; return 0; } strcpy((char *)p,q->gentype); p += strlen(q->gentype)+1; p += store_int(q->lval,4,p); p += store_int(q->kval,4,p); p += store_int(q->seed,4,p); p += store_int(q->init_seed,4,p); p += store_int(q->stream_number,4,p); p += store_intarray(q->si,q->lval-1,4,p); p += store_intarray(q->r0,q->lval,4,p); p += store_intarray(q->r1,q->lval,4,p); p += store_int(q->hptr,4,p); *buffer = (char *) initp; assert(p-initp == size); return p-initp; } #ifdef __STDC__ int *unpack_rng( char *p) #else int *unpack_rng(p) char *p; #endif { int doexit=0,i, found, length, k, param; struct rngen *q; unsigned seed, lag1, lag2; unsigned char *packed; packed = (unsigned char *) p; if(strcmp((char *)packed,GENTYPE) != 0) { fprintf(stderr,"ERROR: Unpacked ' %.24s ' instead of ' %s '\n", packed, GENTYPE); return NULL; } packed += strlen(GENTYPE)+1; packed += load_int(packed,4,&lag1); packed += load_int(packed,4,&lag2); packed += load_int(packed,4,&seed); /* check values of parameters for consistency */ for(i=found=0; igentype = GENTYPE; q->si = (unsigned *) mymalloc((length-1)*sizeof(unsigned)); q->r0 = (unsigned *) mymalloc(length*sizeof(unsigned)); q->r1 = (unsigned *) mymalloc(length*sizeof(unsigned)); if (q->r1 == NULL || q->si == NULL || q->r0 == NULL) return NULL; q->lval = length; q->kval = k; q->seed = seed; q->param = param; packed += load_int(packed,4,(unsigned int *)&q->init_seed); packed += load_int(packed,4,(unsigned int *)&q->stream_number); packed += load_intarray(packed,length-1,4,q->si); packed += load_intarray(packed,length,4,q->r0); packed += load_intarray(packed,length,4,q->r1); packed += load_int(packed,4,(unsigned int *)&q->hptr); NGENS++; return (int *) q; } /*************************************************************************/ /*************************************************************************/ /* FREE_RNG: remove memory for a generator */ /*************************************************************************/ /*************************************************************************/ #ifdef __STDC__ int free_rng(int *genptr) #else int free_rng(genptr) int *genptr; #endif { struct rngen *q; q = (struct rngen *)genptr; free(q->si); free(q->r0); free(q->r1); free(q); NGENS--; return NGENS; } #ifdef __STDC__ int print_rng( int *igen) #else int print_rng(igen) int *igen; #endif { struct rngen *gen; gen = (struct rngen *) igen; printf("\n%s\n", GENTYPE+2); printf("\n \tseed = %d, stream_number = %d\tparameter = %d\n\n", gen->init_seed, gen->stream_number, gen->param); return 1; } /* HAS ;-) */ #if 0 #include "simple_.h" #include "../fwrap_.h" #endif tree-puzzle-5.2/src/sprng/makeseed.c0000644000076400001440000000124407754747631013216 #include #ifdef __STDC__ int make_new_seed() #else int make_new_seed() #endif { time_t tp; struct tm *temp; unsigned int temp2, temp3; static unsigned int temp4 = 0xe0e1; time(&tp); temp = localtime(&tp); temp2 = (temp->tm_sec<<26)+(temp->tm_min<<20)+(temp->tm_hour<<15)+ (temp->tm_mday<<10)+(temp->tm_mon<<6); temp3 = (temp->tm_year<<13)+(temp->tm_wday<<10)+(temp->tm_yday<<1)+ temp->tm_isdst; temp2 ^= clock()^temp3; temp4 = (temp4*0xeeee)%0xffff; temp2 ^= temp4<<16; temp4 = (temp4*0xaeee)%0xffff; temp2 ^= temp4; temp2 &= 0x7fffffff; return temp2; } #if 0 main() { printf("%u\n", make_new_seed()); } #endif tree-puzzle-5.2/src/sprng/lcg64.c0000644000076400001440000004033107756425667012363 /*************************************************************************/ /*************************************************************************/ /* Parallel 64-bit Linear Congruential Generator */ /* */ /* Author: Ashok Srinivasan, */ /* NCSA, University of Illinois, Urbana-Champaign */ /* E-Mail: ashoks@ncsa.uiuc.edu */ /* */ /* Note: The modulus is 2^64 */ /* */ /* Disclaimer: NCSA expressly disclaims any and all warranties, expressed*/ /* or implied, concerning the enclosed software. The intent in sharing */ /* this software is to promote the productive interchange of ideas */ /* throughout the research community. All software is furnished on an */ /* "as is" basis. No further updates to this software should be */ /* expected. Although this may occur, no commitment exists. The authors */ /* certainly invite your comments as well as the reporting of any bugs. */ /* NCSA cannot commit that any or all bugs will be fixed. */ /*************************************************************************/ /*************************************************************************/ /* This is version 1.0, created 20 May 1998 */ #include #include #include #include #define NDEBUG #include #include "memory.h" #include "interface.h" #include "primes-lcg64.h" #include "store.h" #define VERSION "00" /*** Name for Generator ***/ #define GENTYPE VERSION "64 bit Linear Congruential Generator with Prime Addend" int MAX_STREAMS = (146138719); /*** Maximum number of independent streams ***/ #define NPARAMS 3 /*** number of valid parameters ***/ #if LONG_MAX > 2147483647L #if LONG_MAX > 35184372088831L #if LONG_MAX >= 9223372036854775807L #define LONG_SPRNG #define LONG64 long /* 64 bit long */ #define store_long64 store_long #define store_long64array store_longarray #define load_long64 load_long #define load_long64array load_longarray #endif #endif #endif #if !defined(LONG_SPRNG) && defined(_LONG_LONG) #define LONG64 long long #define store_long64 store_longlong #define store_long64array store_longlongarray #define load_long64 load_longlong #define load_long64array load_longlongarray #endif unsigned int PARAMLIST[NPARAMS][2] = {{0x87b0b0fdU, 0x27bb2ee6U}, {0xe78b6955U,0x2c6fe96eU}, {0x31a53f85U,0x369dea0fU}}; /*** Change this to the type of generator you are implementing ***/ struct rngen { char *gentype; int stream_number; int nstreams; int init_seed; int parameter; int narrays; int *array_sizes; int **arrays; int spawn_offset; /*** declare other variables here ***/ unsigned int prime; #ifdef LONG64 /* 64 bit integer types */ unsigned LONG64 state, multiplier; #else /* No 64 bit type available, so use array of floats */ double state[3], multiplier[3];/* simulate 64 bit arithmetic */ #endif }; /*************************************************************************/ /* You should not need to look at the next few lines! */ #define INIT_SEED1 0x2bc6ffffU #define INIT_SEED0 0x8cfe166dU #define TWO_M22 2.384185791015625e-07 /* 2^(-22) */ #define TWO_P22 4194304 /* 2^(22) */ #define TWO_M20 9.5367431640625e-07 /* 2^(-20) */ #define TWO_P20 1048576 /* 2^(20) */ #define TWO_M42 2.273736754432321e-13 /* 2^(-42) */ #define TWO_M64 5.4210108624275222e-20 /* 2^(-64) */ /* */ /************************************************************************/ int NGENS=0; /* number of random streams in current process */ /* Initialize random number stream */ #ifdef __STDC__ int *init_rng( int gennum, int total_gen, int seed, int param) #else int *init_rng(gennum,total_gen,seed,param) int gennum,param,seed,total_gen; #endif { /* gives back one stream (node gennum) with updated spawning */ /* info; should be called total_gen times, with different value */ /* of gennum in [0,total_gen) each call */ struct rngen *genptr; int i; double tempdbl; if (total_gen <= 0) /* Is total_gen valid ? */ { total_gen = 1; fprintf(stderr,"WARNING - init_rng: Total_gen <= 0. Default value of 1 used for total_gen\n"); } if (gennum >= MAX_STREAMS) /* check if gen_num is valid */ fprintf(stderr,"WARNING - init_rng: gennum: %d > maximum number of independent streams: %d\n\tIndependence of streams cannot be guranteed.\n", gennum, MAX_STREAMS); if (gennum < 0 || gennum >= total_gen) /* check if gen_num is valid */ { fprintf(stderr,"ERROR - init_rng: gennum %d out of range [%d,%d).\n", gennum, 0, total_gen); return (int *) NULL; } if (param < 0 || param >= NPARAMS) /* check if parameter is valid */ { fprintf(stderr,"WARNING - init_rng: parameter not valid. Using Default parameter.\n"); param = 0; } genptr = (struct rngen *) mymalloc(1*sizeof(struct rngen)); if(genptr == NULL) /* check if memory allocated for data structure */ return NULL; /* Initiallize data structure variables */ genptr->gentype = GENTYPE; genptr->stream_number = gennum; genptr->nstreams = total_gen; genptr->init_seed = seed & 0x7fffffff; /* Only 31 LSB of seed considered */ genptr->parameter = param; genptr->spawn_offset = total_gen; /*** Change the next line depending on your generators data needs ***/ genptr->narrays = 0; /* number of arrays needed by your generator */ if(genptr->narrays > 0) { genptr->array_sizes = (int *) mymalloc(genptr->narrays*sizeof(int)); genptr->arrays = (int **) mymalloc(genptr->narrays*sizeof(int *)); if(genptr->array_sizes == NULL || genptr->arrays == NULL) return NULL; } else { genptr->array_sizes = NULL; genptr->arrays = NULL; } /*** Change the next line depending on your generators data needs ***/ /* initiallize ...array_sizes to the sizes of the arrays */ for(i=0; inarrays; i++) { genptr->arrays[i] = (int *) mymalloc(genptr->array_sizes[i]*sizeof(int)); if(genptr->arrays[i] == NULL) /* check if memory allocated for data structure */ return NULL; } /*** Add initialization statements for your data in the arrays and other variables you have defined ***/ getprime(1,&genptr->prime,gennum); #ifdef LONG64 genptr->multiplier = ((unsigned LONG64) PARAMLIST[param][1])<<32 | ((unsigned LONG64) PARAMLIST[param][0]); genptr->state = ( ((unsigned LONG64) INIT_SEED1)<<32 | INIT_SEED0) ^(((unsigned LONG64) seed<<33)|gennum); #else genptr->multiplier[0] = (double) (PARAMLIST[param][0]&0x3fffff); genptr->multiplier[1] = (double) (PARAMLIST[param][0]>>22 | (PARAMLIST[param][1]&0xfff)<<10); genptr->multiplier[2] = (double) (PARAMLIST[param][1]>>12); genptr->state[0] = (double) ((INIT_SEED0^gennum)&0x3fffff); genptr->state[1] = (double) ((INIT_SEED0^gennum)>>22 | ((INIT_SEED1 ^ (unsigned)seed<<1)&0xfff)<<10); genptr->state[2] = (double) ((INIT_SEED1 ^ (unsigned)seed<<1)>>12); #endif for(i=0; i<127*genptr->stream_number; i++) tempdbl = get_rn_dbl((int *) genptr); NGENS++; /* NGENS = # of streams */ return (int *) genptr; } #ifdef LONG64 #define advance_state(genptr) genptr->state = genptr->state*genptr->multiplier + genptr->prime; #else #define advance_state(genptr) {double t0, t1, t2, t3, st0, st1, st2;\ t0 = genptr->state[0]*genptr->multiplier[0] + genptr->prime;\ t1 = (double) (int) (t0*TWO_M22); \ st0 = t0 - TWO_P22*t1; \ assert( (int) st0 == st0); \ t1 += genptr->state[1]*genptr->multiplier[0] + \ genptr->state[0]*genptr->multiplier[1]; \ t2 = (double) (int) (t1*TWO_M22); \ st1 = t1 - TWO_P22*t2; \ assert( (int) st1 == st1); \ t2 += genptr->state[2]*genptr->multiplier[0] + \ genptr->state[1]*genptr->multiplier[1] + \ genptr->state[0]*genptr->multiplier[2];\ t3 = (double) (int) (t2*TWO_M20); \ st2 = t2 - TWO_P20*t3; \ assert( (int) st2 == st2); \ genptr->state[0] = st0; \ genptr->state[1] = st1; \ genptr->state[2] = st2;} #endif /* Returns a double precision random number */ #ifdef __STDC__ double get_rn_dbl(int *igenptr) #else double get_rn_dbl(igenptr) int *igenptr; #endif { struct rngen *genptr = (struct rngen *) igenptr; #ifdef LONG64 #ifdef _LONG_LONG #define EXPO 0x3ff0000000000000ULL #else #define EXPO 0x3ff0000000000000UL #endif static double dtemp[1] = {0.0}; advance_state(genptr); /* next state in sequence */ #if defined(CONVEX) || defined(O2K) || defined(SGI) || defined(GENERIC) *((unsigned LONG64 *) dtemp) = (genptr->state>>12) | EXPO; return *dtemp - (double) 1.0; #else return genptr->state*TWO_M64; #endif #else /* 32 bit machine */ #define EXPO 0x3ff00000 #ifdef LittleEndian #define MSB 1 #else #define MSB 0 #endif #define LSB (1-MSB) double ans; unsigned int ist0, ist1, ist2; static double temp[1] = {0.0}; advance_state(genptr); /* next state in sequence */ ist0 = genptr->state[0]; ist1 = genptr->state[1]; ist2 = genptr->state[2]; #if defined(HP) || defined(SUN) || defined(SOLARIS) || defined(GENERIC) /*IEEE mantissa is 52 bits. */ ((unsigned int *)temp)[LSB] = ist1<<10 | ist0>>12; ((unsigned int *)temp)[MSB] = EXPO | ist2; return *temp - (double) 1.0; #else return genptr->state[2]*TWO_M20 + genptr->state[1]*TWO_M42 + genptr->state[0]*TWO_M64; #endif #endif } /* Return a random integer */ #ifdef __STDC__ int get_rn_int(int *igenptr) #else int get_rn_int(igenptr) int *igenptr; #endif { #ifdef LONG64 struct rngen *genptr = (struct rngen *) igenptr; advance_state(genptr); /* next state in sequence */ return genptr->state>>33; #else return (int) (get_rn_dbl(igenptr)*0x80000000U); #endif } /* Return a single precision random number */ #ifdef __STDC__ float get_rn_flt(int *igenptr) #else float get_rn_flt(igenptr) int *igenptr; #endif { /* If you have a more efficient way of computing the random integer, then please replace the statement below with your scheme. */ return (float) get_rn_dbl(igenptr); } /*************************************************************************/ /*************************************************************************/ /* SPAWN_RNG: spawns new generators */ /*************************************************************************/ /*************************************************************************/ #ifdef __STDC__ int spawn_rng(int *igenptr, int nspawned, int ***newgens, int checkid) #else int spawn_rng(igenptr,nspawned, newgens, checkid) int *igenptr,nspawned, ***newgens, checkid; #endif { struct rngen **genptr, *tempptr = (struct rngen *) igenptr; int i, j; if (nspawned <= 0) /* is nspawned valid ? */ { nspawned = 1; fprintf(stderr,"WARNING - spawn_rng: nspawned <= 0. Default value of 1 used for nspawned\n"); } genptr = (struct rngen **) mymalloc(nspawned*sizeof(struct rngen *)); if(genptr == NULL) /* allocate memory for pointers to structures */ { *newgens = NULL; return 0; } for(i=0; istream_number + tempptr->spawn_offset*(i+1); if(gennum > MAX_STREAMS) /* change seed to avoid repeating sequence */ seed = (tempptr->init_seed)^gennum; else seed = tempptr->init_seed; /* Initialize a stream. This stream has incorrect spawning information. But we will correct it below. */ genptr[i] = (struct rngen *) init_rng(gennum, gennum+1, seed, tempptr->parameter); if(genptr[i] == NULL) /* Was generator initiallized? */ { nspawned = i; break; } genptr[i]->spawn_offset = (nspawned+1)*tempptr->spawn_offset; } tempptr->spawn_offset *= (nspawned+1); *newgens = (int **) genptr; if(checkid != 0) for(i=0; inarrays; i++) free(q->arrays[i]); if(q->narrays > 0) { free(q->array_sizes); free(q->arrays); } free(q); NGENS--; return NGENS; } #ifdef __STDC__ int pack_rng( int *genptr, char **buffer) #else int pack_rng(genptr,buffer) int *genptr; char **buffer; #endif { unsigned char *p, *initp; int size, i; unsigned int temp, m[2]; struct rngen *q; q = (struct rngen *) genptr; size = 48 + strlen(q->gentype)+1; initp = p = (unsigned char *) mymalloc(size); /* allocate memory */ /* The new load/store routines make using sizeof unnecessary. Infact, */ /* using sizeof could be erroneous. */ if(p == NULL) { *buffer = NULL; return 0; } strcpy((char *)p,q->gentype); p += strlen(q->gentype)+1; p += store_int(q->stream_number,4,p); p += store_int(q->nstreams,4,p); p += store_int(q->init_seed,4,p); p += store_int(q->parameter,4,p); p += store_int(q->narrays,4,p); p += store_int(q->spawn_offset,4,p); p += store_int(q->prime,4,p); #ifdef LONG64 /* 64 bit integer types */ p += store_long64(q->state,8,p); p += store_long64(q->multiplier,8,p); #else /* No 64 bit type available */ m[0] = q->state[2]; temp = q->state[1];m[0]=(m[0]<<12)|(temp>>10); m[1] = q->state[1]; temp = q->state[0];m[1]=(m[1]<<22)|(temp); p += store_intarray(m,2,4,p); m[0] = q->multiplier[2]; temp = q->multiplier[1];m[0]=(m[0]<<12)|(temp>>10); m[1] = q->multiplier[1]; temp = q->multiplier[0];m[1]=(m[1]<<22)|(temp); p += store_intarray(m,2,4,p); #endif *buffer = (char *) initp; assert(p-initp == size); return p-initp; } #ifdef __STDC__ int *unpack_rng( char *packed) #else int *unpack_rng(packed) char *packed; #endif { struct rngen *q; unsigned int i, m[2]; unsigned char *p; p = (unsigned char *) packed; q = (struct rngen *) mymalloc(sizeof(struct rngen)); if(q == NULL) return NULL; if(strcmp((char *)p,GENTYPE) != 0) { fprintf(stderr,"ERROR: Unpacked ' %.24s ' instead of ' %s '\n", p, GENTYPE); return NULL; } else q->gentype = GENTYPE; p += strlen(q->gentype)+1; p += load_int(p,4,(unsigned int *)&q->stream_number); p += load_int(p,4,(unsigned int *)&q->nstreams); p += load_int(p,4,(unsigned int *)&q->init_seed); p += load_int(p,4,(unsigned int *)&q->parameter); p += load_int(p,4,(unsigned int *)&q->narrays); p += load_int(p,4,(unsigned int *)&q->spawn_offset); p += load_int(p,4,&q->prime); #ifdef LONG64 /* 64 bit integer types */ p += load_long64(p,8,&q->state); p += load_long64(p,8,&q->multiplier); #else /* No 64 bit type available */ p += load_intarray(p,2,4,m); q->state[0] = (double) (m[1]&0x3fffff); q->state[1] = (double) ((m[1]>>22) | (m[0]&0xfff)<<10); q->state[2] = (double) (m[0]>>12); p += load_intarray(p,2,4,m); q->multiplier[0] = (double) (m[1]&0x3fffff); q->multiplier[1] = (double) ((m[1]>>22) | (m[0]&0xfff)<<10); q->multiplier[2] = (double) (m[0]>>12); #endif q->array_sizes = NULL; q->arrays = NULL; NGENS++; return (int *) q; } #ifdef __STDC__ int get_seed_rng(int *gen) #else int get_seed_rng(gen) int *gen; #endif { return ((struct rngen *) gen)->init_seed; } #ifdef __STDC__ int print_rng( int *igen) #else int print_rng(igen) int *igen; #endif { struct rngen *gen; printf("\n%s\n", GENTYPE+2); gen = (struct rngen *) igen; printf("\n \tseed = %d, stream_number = %d\tparameter = %d\n\n", gen->init_seed, gen->stream_number, gen->parameter); return 1; } /* HAS ;-) */ #if 0 #include "simple_.h" #include "fwrap_.h" #endif tree-puzzle-5.2/src/sprng/README0000644000076400001440000000043610071222064012124 The original source files are from the SPRNG (Scalable Pseudo Random Number Generator) library package. Mascagni, Michael and Srinivasan, Ashok (2000) SPRNG: A Scalable Library for Pseudorandom Number Generation. ACM Trans. Math. Software, 26:436-461, DOI: 10.1145/358407.358427 tree-puzzle-5.2/src/sprng/multiply.h0000644000076400001440000000154007755111550013305 /* used by lcg */ #ifdef LONG64 #define mult_48_64(a,b,c) c = (a*b); #define multiply(genptr) mult_48_64(genptr->seed,genptr->multiplier,genptr->seed); genptr->seed += genptr->prime; genptr->seed &= LSB48; #else #define mult_48_32(a,b,c) c[0] = a[0]*b[0]; c[1] = a[1]*b[0]+a[0]*b[1];\ c[2] = a[0]*b[2]+a[1]*b[1]+a[2]*b[0];\ c[3] = a[3]*b[0]+a[2]*b[1]+a[1]*b[2]+a[0]*b[3]; #define multiply(genptr,m,s,res) s[3] = (unsigned int) genptr->seed[0] >> 12;\ s[2] = genptr->seed[0] & 4095; s[1] = genptr->seed[1] >> 12;\ s[0] = genptr->seed[1] & 4095;\ mult_48_32(m,s,res);\ genptr->seed[1] = res[0] + ((res[1]&4095) << 12) + genptr->prime;\ genptr->seed[0] = ( (unsigned int) genptr->seed[1] >> 24)\ + res[2] + ((unsigned int) res[1] >> 12 ) + (res[3] << 12);\ genptr->seed[1] &= 16777215; genptr->seed[0] &= 16777215; #endif tree-puzzle-5.2/src/sprng/primes-lcg64.c0000644000076400001440000000545707755107642013657 #include #include #include "primes-lcg64.h" #include "primelist-lcg64.h" #define YES 1 #define NO 0 #define NPRIMES 10000 int primes[NPRIMES]; #ifdef __STDC__ int init_prime(void) #else int init_prime() #endif { int i, j, obtained = 0, isprime; for(i=3; i < MINPRIME; i += 2) { isprime = YES; for(j=0; j < obtained; j++) if(i%primes[j] == 0) { isprime = NO; break; } else if(primes[j]*primes[j] > i) break; if(isprime == YES) { primes[obtained] = i; obtained++; } } return obtained; } #ifdef __STDC__ int getprime(int need, unsigned int *prime_array, int offset) #else int getprime(need, prime_array, offset) int need, offset; unsigned int *prime_array; #endif { static int initiallized = NO, num_prime; unsigned int largest; int i, isprime, index, obtained = 0; if(need <= 0) { fprintf(stderr,"WARNING: Number of primes needed = %d < 1; None returned\n" , need); return 0; } if(offset < 0) { fprintf(stderr,"WARNING: Offset of prime = %d < 1; None returned\n" , offset); return 0; } if(offset+need-1 MAXPRIMEOFFSET) { fprintf(stderr,"WARNING: generator has branched maximum number of times;\nindependence of generators no longer guaranteed"); offset = offset % MAXPRIMEOFFSET; } if(offset < PRIMELISTSIZE1) /* search table for previous prime */ { largest = prime_list[offset] + 2; offset = 0; } else { index = (unsigned int) ((offset-PRIMELISTSIZE1+1)/STEP) + PRIMELISTSIZE1 - 1; largest = prime_list[index] + 2; offset -= (index-PRIMELISTSIZE1+1)*STEP + PRIMELISTSIZE1 - 1; } while(need > obtained && largest > MINPRIME) { isprime = YES; largest -= 2; for(i=0; i 0) offset--; else if(isprime == YES) prime_array[obtained++] = largest; } if(need > obtained) fprintf(stderr,"ERROR: Insufficient number of primes: needed %d, obtained %d\n", need, obtained); return obtained; } #if 0 main() { unsigned int newprimes[1500], np, i; np = getprime(2,newprimes,0); np = getprime(2,newprimes+2,9); np = getprime(2,newprimes+4,12); for(i=0; i<6; i++) printf("%u. %u \n", i, newprimes[i]); /*while(np--) printf("New primes: %u\n", newprimes[np]); np = getprime(5,newprimes); printf("%d new primes obtained ...\n", np); while(np--) printf("New primes: %u\n", newprimes[np]);*/ } #endif tree-puzzle-5.2/src/sprng/primes-lcg64.h0000644000076400001440000000065107755107654013656 #ifndef _primes64_h_ #define _primes64_h_ #ifndef ANSI_ARGS #ifdef __STDC__ #define ANSI_ARGS(args) args #else #define ANSI_ARGS(args) () #endif #endif int getprime ANSI_ARGS((int need, unsigned int *prime_array, int offset)); #define MAXPRIME 3037000501U /* largest odd # < sqrt(2)*2^31+2 */ #define MINPRIME 55108 /* sqrt(MAXPRIME) */ #define MAXPRIMEOFFSET 146138719U /* Total number of available primes */ #endif tree-puzzle-5.2/src/sprng/sprng.h0000644000076400001440000000371707756427656012611 #ifndef _sprng_h_ #define _sprng_h_ #include "interface.h" #define SPRNG_DEFAULT 0 #define CRAYLCG 0 #define DRAND48 1 #define FISH1 2 #define FISH2 3 #define FISH3 4 #define FISH4 5 #define FISH5 6 #define LECU1 0 #define LECU2 1 #define LECU3 2 #define LAG1279 0 #define LAG17 1 #define LAG31 2 #define LAG55 3 #define LAG63 4 #define LAG127 5 #define LAG521 6 #define LAG521B 7 #define LAG607 8 #define LAG607B 9 #define LAG1279B 10 #define CHECK 1 #define MAX_PACKED_LENGTH 24000 #ifdef SPRNG_USE_MPI #define MPINAME(A) A ## _mpi #else #define MPINAME(A) A #endif #define make_sprng_seed MPINAME(make_new_seed) #if defined(SIMPLE_SPRNG) /* HAS ;-) */ #if 0 #define pack_sprng pack_rng_simple #define unpack_sprng unpack_rng_simple #define isprng MPINAME(get_rn_int_simple) #define init_sprng MPINAME(init_rng_simple) #define print_sprng print_rng_simple #ifdef FLOAT_GEN #define sprng MPINAME(get_rn_flt_simple) #else #define sprng MPINAME(get_rn_dbl_simple) #endif #endif #elif !defined(CHECK_POINTERS) #define free_sprng free_rng #define pack_sprng pack_rng #define unpack_sprng unpack_rng #define isprng get_rn_int #define spawn_sprng(A,B,C) spawn_rng(A,B,C,!CHECK) #define init_sprng init_rng #define print_sprng print_rng #ifdef FLOAT_GEN #define sprng get_rn_flt #else #define sprng get_rn_dbl #endif #else /* HAS ;-) */ #if 0 #define free_sprng(A) ((deleteID(A)==NULL) ? -1 : free_rng(A)) #define pack_sprng(A,B) ((checkID(A)==NULL) ? 0 : pack_rng(A,B)) #define unpack_sprng(A) addID(unpack_rng(A)) #define isprng(A) ((checkID(A)==NULL) ? -1 : get_rn_int(A)) #define spawn_sprng(A,B,C) ((checkID(A)==NULL) ? 0 : spawn_rng(A,B,C,CHECK)) #define init_sprng(A,B,C,D) addID(init_rng(A,B,C,D)) #define print_sprng(A) ((checkID(A)==NULL) ? 0 : print_rng(A)) #ifdef FLOAT_GEN #define sprng(A) ((checkID(A)==NULL) ? -1.0 : get_rn_flt(A)) #else #define sprng(A) ((checkID(A)==NULL) ? -1.0 : get_rn_dbl(A)) #endif #endif #endif #endif tree-puzzle-5.2/src/sprng/primes-lcg.c0000644000076400001440000000535707755107561013504 #include #include #include "primes-lcg.h" #include "primelist-lcg.h" #define YES 1 #define NO 0 #define NPRIMES 1000 int primes[NPRIMES]; #ifdef __STDC__ int init_prime(void) #else int init_prime() #endif { int i, j, obtained = 0, isprime; for(i=3; i < MINPRIME; i += 2) { isprime = YES; for(j=0; j < obtained; j++) if(i%primes[j] == 0) { isprime = NO; break; } else if(primes[j]*primes[j] > i) break; if(isprime == YES) { primes[obtained] = i; obtained++; } } return obtained; } #ifdef __STDC__ int getprime(int need, int *prime_array, int offset) #else int getprime(need, prime_array, offset) int need, *prime_array,offset; #endif { static int initiallized = NO, num_prime; int largest; int i, isprime, index, obtained = 0; if(need <= 0) { fprintf(stderr,"WARNING: Number of primes needed = %d < 1; None returned\n" , need); return 0; } if(offset < 0) { fprintf(stderr,"WARNING: Offset of prime = %d < 1; None returned\n" , offset); return 0; } if(offset+need-1 MAXPRIMEOFFSET) { fprintf(stderr,"WARNING: generator has branched maximum number of times;\nindependence of generators no longer guaranteed"); offset = offset % MAXPRIMEOFFSET; } if(offset < PRIMELISTSIZE1) /* search table for previous prime */ { largest = prime_list[offset] + 2; offset = 0; } else { index = (int) ((offset-PRIMELISTSIZE1+1)/STEP) + PRIMELISTSIZE1 - 1; largest = prime_list[index] + 2; offset -= (index-PRIMELISTSIZE1+1)*STEP + PRIMELISTSIZE1 - 1; } while(need > obtained && largest > MINPRIME) { isprime = YES; largest -= 2; for(i=0; i 0) offset--; else if(isprime == YES) prime_array[obtained++] = largest; } if(need > obtained) fprintf(stderr,"ERROR: Insufficient number of primes: needed %d, obtained %d\n", need, obtained); return obtained; } #if 0 main() { int newprimes[1500], np, i; np = getprime(2,newprimes,0); np = getprime(2,newprimes+2,9); np = getprime(2,newprimes+4,12); for(i=0; i<6; i++) printf("%d. %d \n", i, newprimes[i]); /*while(np--) printf("New primes: %d\n", newprimes[np]); np = getprime(5,newprimes); printf("%d new primes obtained ...\n", np); while(np--) printf("New primes: %d\n", newprimes[np]);*/ } #endif tree-puzzle-5.2/src/sprng/primes-lcg.h0000644000076400001440000000053707755106031013473 #ifndef _primes_h_ #define _primes_h_ #ifndef ANSI_ARGS #ifdef __STDC__ #define ANSI_ARGS(args) args #else #define ANSI_ARGS(args) () #endif #endif int getprime ANSI_ARGS((int need, int *prime_array, int offset)); #define MAXPRIME 11863285 /* sqrt(2)*2^23 + 2 */ #define MINPRIME 3444 /* sqrt(MAXPRIME) */ #define MAXPRIMEOFFSET 779156 #endif tree-puzzle-5.2/src/sprng/store.c0000644000076400001440000000553507754747671012607 #include #include "store.h" int store_long(unsigned long l, int nbytes, unsigned char *c) { int i; for(i=0; i>(8*(nbytes-i-1)))&0xff; return nbytes; /* return number of chars filled */ } int store_longarray(unsigned long *l, int n, int nbytes, unsigned char *c) { int i; for(i=0; i>(8*(nbytes-i-1)))&0xff; return nbytes; /* return number of chars filled */ } int store_longlongarray(unsigned long long *l, int n, int nbytes, unsigned char *c) { int i; for(i=0; i>(8*(nbytes-i-1)))&0xff; return nbytes; /* return number of chars filled */ } int store_intarray(unsigned int *l, int n, int nbytes, unsigned char *c) { int i; for(i=0; i #include #include #include #define NDEBUG #include #include "memory.h" #include "interface.h" #include "primes-lcg64.h" #include "store.h" #define VERSION "00" /*** Name for Generator ***/ #define GENTYPE VERSION "Combined multiple recursive generator" int MAX_STREAMS = (146138719); /*** Maximum number of independent streams ***/ #define NPARAMS 3 /*** number of valid parameters ***/ #if LONG_MAX > 2147483647L #if LONG_MAX > 35184372088831L #if LONG_MAX >= 9223372036854775807L #define LONG_SPRNG #define LONG64 long /* 64 bit long */ #define store_long64 store_long #define store_long64array store_longarray #define load_long64 load_long #define load_long64array load_longarray #endif #endif #endif #if !defined(LONG_SPRNG) && defined(_LONG_LONG) #define LONG64 long long #define store_long64 store_longlong #define store_long64array store_longlongarray #define load_long64 load_longlong #define load_long64array load_longlongarray #endif unsigned int PARAMLIST[NPARAMS][2] = {{0x87b0b0fdU, 0x27bb2ee6U}, {0xe78b6955U,0x2c6fe96eU}, {0x31a53f85U,0x369dea0fU}}; /*** Change this to the type of generator you are implementing ***/ struct rngen { char *gentype; int stream_number; int nstreams; int init_seed; int parameter; int narrays; int *array_sizes; int **arrays; int spawn_offset; /*** declare other variables here ***/ unsigned int prime; #ifdef LONG64 /* 64 bit integer types */ unsigned LONG64 state, multiplier; unsigned LONG64 s0, s1, s2, s3, s4; #else /* No 64 bit type available, so use array of floats */ double state[3], multiplier[3];/* simulate 64 bit arithmetic */ int s0, s1, s2, s3, s4; #endif }; /*************************************************************************/ /* You should not need to look at the next few lines! */ #define INIT_SEED1 0x2bc6ffffU #define INIT_SEED0 0x8cfe166dU #define TWO_M22 2.384185791015625e-07 /* 2^(-22) */ #define TWO_P22 4194304 /* 2^(22) */ #define TWO_M20 9.5367431640625e-07 /* 2^(-20) */ #define TWO_P20 1048576 /* 2^(20) */ #define TWO_M42 2.273736754432321e-13 /* 2^(-42) */ #define TWO_M64 5.4210108624275222e-20 /* 2^(-64) */ /* */ /************************************************************************/ int NGENS=0; /* number of random streams in current process */ /* Initialize random number stream */ #ifdef __STDC__ int *init_rng( int gennum, int total_gen, int seed, int param) #else int *init_rng(gennum,total_gen,seed,param) int gennum,param,seed,total_gen; #endif { /* gives back one stream (node gennum) with updated spawning */ /* info; should be called total_gen times, with different value */ /* of gennum in [0,total_gen) each call */ struct rngen *genptr; int i; double tempdbl; if (total_gen <= 0) /* Is total_gen valid ? */ { total_gen = 1; fprintf(stderr,"WARNING - init_rng: Total_gen <= 0. Default value of 1 used for total_gen\n"); } if (gennum >= MAX_STREAMS) /* check if gen_num is valid */ fprintf(stderr,"WARNING - init_rng: gennum: %d > maximum number of independent streams: %d\n\tIndependence of streams cannot be guranteed.\n", gennum, MAX_STREAMS); if (gennum < 0 || gennum >= total_gen) /* check if gen_num is valid */ { fprintf(stderr,"ERROR - init_rng: gennum %d out of range [%d,%d).\n", gennum, 0, total_gen); return (int *) NULL; } if (param < 0 || param >= NPARAMS) /* check if parameter is valid */ { fprintf(stderr,"WARNING - init_rng: parameter not valid. Using Default parameter.\n"); param = 0; } genptr = (struct rngen *) mymalloc(1*sizeof(struct rngen)); if(genptr == NULL) /* check if memory allocated for data structure */ return NULL; /* Initiallize data structure variables */ genptr->gentype = GENTYPE; genptr->stream_number = gennum; genptr->nstreams = total_gen; genptr->init_seed = seed & 0x7fffffff; /* Only 31 LSB of seed considered */ genptr->parameter = param; genptr->spawn_offset = total_gen; /*** Change the next line depending on your generators data needs ***/ genptr->narrays = 0; /* number of arrays needed by your generator */ if(genptr->narrays > 0) { genptr->array_sizes = (int *) mymalloc(genptr->narrays*sizeof(int)); genptr->arrays = (int **) mymalloc(genptr->narrays*sizeof(int *)); if(genptr->array_sizes == NULL || genptr->arrays == NULL) return NULL; } else { genptr->array_sizes = NULL; genptr->arrays = NULL; } /*** Change the next line depending on your generators data needs ***/ /* initiallize ...array_sizes to the sizes of the arrays */ for(i=0; inarrays; i++) { genptr->arrays[i] = (int *) mymalloc(genptr->array_sizes[i]*sizeof(int)); if(genptr->arrays[i] == NULL) /* check if memory allocated for data structure */ return NULL; } /*** Add initialization statements for your data in the arrays and other variables you have defined ***/ getprime(1,&genptr->prime,gennum); #ifdef LONG64 genptr->multiplier = ((unsigned LONG64) PARAMLIST[param][1])<<32 | ((unsigned LONG64) PARAMLIST[param][0]); genptr->state = ( ((unsigned LONG64) INIT_SEED1)<<32 | INIT_SEED0) ^(((unsigned LONG64) seed<<33)|gennum); #else genptr->multiplier[0] = (double) (PARAMLIST[param][0]&0x3fffff); genptr->multiplier[1] = (double) (PARAMLIST[param][0]>>22 | (PARAMLIST[param][1]&0xfff)<<10); genptr->multiplier[2] = (double) (PARAMLIST[param][1]>>12); genptr->state[0] = (double) ((INIT_SEED0^gennum)&0x3fffff); genptr->state[1] = (double) ((INIT_SEED0^gennum)>>22 | ((INIT_SEED1 ^ (unsigned)seed<<1)&0xfff)<<10); genptr->state[2] = (double) ((INIT_SEED1 ^ (unsigned)seed<<1)>>12); #endif genptr->s0 = genptr->s1 = genptr->s2 = genptr->s3 = genptr->s4 = /*0xfffffff*/ 0x1; for(i=0; i<127*genptr->stream_number; i++) tempdbl = get_rn_dbl((int *) genptr); NGENS++; /* NGENS = # of streams */ return (int *) genptr; } #ifdef LONG64 #define advance_state(genptr) genptr->state = genptr->state*genptr->multiplier + genptr->prime; #else #define advance_state(genptr) {double t0, t1, t2, t3, st0, st1, st2;\ t0 = genptr->state[0]*genptr->multiplier[0] + genptr->prime;\ t1 = (double) (int) (t0*TWO_M22); \ st0 = t0 - TWO_P22*t1; \ assert( (int) st0 == st0); \ t1 += genptr->state[1]*genptr->multiplier[0] + \ genptr->state[0]*genptr->multiplier[1]; \ t2 = (double) (int) (t1*TWO_M22); \ st1 = t1 - TWO_P22*t2; \ assert( (int) st1 == st1); \ t2 += genptr->state[2]*genptr->multiplier[0] + \ genptr->state[1]*genptr->multiplier[1] + \ genptr->state[0]*genptr->multiplier[2];\ t3 = (double) (int) (t2*TWO_M20); \ st2 = t2 - TWO_P20*t3; \ assert( (int) st2 == st2); \ genptr->state[0] = st0; \ genptr->state[1] = st1; \ genptr->state[2] = st2;} #endif #define m1 2147483647 #define a0 107374182 #define a4 104480 #define q0 20 #define q4 20554 #define r0 7 #define r4 1727 #ifdef LONG64 #define advance_cmrg(genptr) {unsigned LONG64 p;\ advance_state(genptr);\ p = a0*genptr->s0 + a4*genptr->s4;\ p = (p>>31) + (p&0x7fffffff);\ if(p&0x80000000) p = (p+1)&0x7fffffff;\ genptr->s4=genptr->s3; genptr->s3=genptr->s2;genptr->s2=genptr->s1;genptr->s1=genptr->s0;genptr->s0=p;} #else #define advance_cmrg(genptr) {int h, p0, p4;\ advance_state(genptr);\ h=genptr->s4/q4;p4=a4*(genptr->s4-h*q4)-h*r4;\ genptr->s4=genptr->s3;genptr->s3=genptr->s2;genptr->s2=genptr->s1;genptr->s1=genptr->s0;\ h=genptr->s0/q0; p0=a0*(genptr->s0-h*q0)-h*r0;\ if(p0<0) p0+=m1; if(p4>0)p4-=m1;\ genptr->s0=p0+p4; if(genptr->s0<0) genptr->s0+=m1;} #endif /* Returns a double precision random number */ #ifdef __STDC__ double get_rn_dbl(int *igenptr) #else double get_rn_dbl(igenptr) int *igenptr; #endif { struct rngen *genptr = (struct rngen *) igenptr; #ifdef LONG64 #ifdef _LONG_LONG #define EXPO 0x3ff0000000000000ULL #define MULT_MASK 0xffffffffffffffffULL #else #define EXPO 0x3ff0000000000000UL #define MULT_MASK 0xffffffffffffffffUL #endif static double dtemp[1] = {0.0}; advance_cmrg(genptr); #if defined(CONVEX) || defined(O2K) || defined(SGI) || defined(GENERIC) *((unsigned LONG64 *) dtemp) = (((genptr->state+(genptr->s0<<32))&MULT_MASK)>>12) | EXPO; return *dtemp - (double) 1.0; #else return ((genptr->state+(genptr->s0<<32))&MULT_MASK)*TWO_M64; #endif #else /* 32 bit machine */ #define EXPO 0x3ff00000 #ifdef LittleEndian #define MSB 1 #else #define MSB 0 #endif #define LSB (1-MSB) double ans; unsigned int ist0, ist1, ist2, tempi, tempi2; static double temp[1] = {0.0}; advance_cmrg(genptr); ist0 = genptr->state[0]; ist1 = genptr->state[1]; ist2 = genptr->state[2]; tempi2 = ist2<<12 | ist1>>10; tempi = (genptr->s0+tempi2)&0xffffffff; /* add modulo 2^64 */ ist1 = (ist1&0x3ff) | (tempi&0xfff)<<10; ist2 = tempi>>12; #if defined(HP) || defined(SUN) || defined(SOLARIS) || defined(GENERIC) /*IEEE mantissa is 52 bits. */ ((unsigned int *)temp)[LSB] = (ist1<<10 | ist0>>12); ((unsigned int *)temp)[MSB] = EXPO | ist2; return *temp - (double) 1.0; #else return ist2*TWO_M20 + ist1*TWO_M42 + ist0*TWO_M64; #endif #endif } /* Return a random integer */ #ifdef __STDC__ int get_rn_int(int *igenptr) #else int get_rn_int(igenptr) int *igenptr; #endif { #ifdef LONG64 struct rngen *genptr = (struct rngen *) igenptr; advance_cmrg(genptr); return ((genptr->state+(genptr->s0<<32))&MULT_MASK)>>33; #else return (int) (get_rn_dbl(igenptr)*0x80000000U); #endif } /* Return a single precision random number */ #ifdef __STDC__ float get_rn_flt(int *igenptr) #else float get_rn_flt(igenptr) int *igenptr; #endif { /* If you have a more efficient way of computing the random integer, then please replace the statement below with your scheme. */ return (float) get_rn_dbl(igenptr); } #undef m1 #undef a0 #undef a4 #undef q0 #undef q4 #undef r0 #undef r4 /*************************************************************************/ /*************************************************************************/ /* SPAWN_RNG: spawns new generators */ /*************************************************************************/ /*************************************************************************/ #ifdef __STDC__ int spawn_rng(int *igenptr, int nspawned, int ***newgens, int checkid) #else int spawn_rng(igenptr,nspawned, newgens, checkid) int *igenptr,nspawned, ***newgens, checkid; #endif { struct rngen **genptr, *tempptr = (struct rngen *) igenptr; int i, j; if (nspawned <= 0) /* is nspawned valid ? */ { nspawned = 1; fprintf(stderr,"WARNING - spawn_rng: nspawned <= 0. Default value of 1 used for nspawned\n"); } genptr = (struct rngen **) mymalloc(nspawned*sizeof(struct rngen *)); if(genptr == NULL) /* allocate memory for pointers to structures */ { *newgens = NULL; return 0; } for(i=0; istream_number + tempptr->spawn_offset*(i+1); if(gennum > MAX_STREAMS) /* change seed to avoid repeating sequence */ seed = (tempptr->init_seed)^gennum; else seed = tempptr->init_seed; /* Initialize a stream. This stream has incorrect spawning information. But we will correct it below. */ genptr[i] = (struct rngen *) init_rng(gennum, gennum+1, seed, tempptr->parameter); if(genptr[i] == NULL) /* Was generator initiallized? */ { nspawned = i; break; } genptr[i]->spawn_offset = (nspawned+1)*tempptr->spawn_offset; } tempptr->spawn_offset *= (nspawned+1); *newgens = (int **) genptr; if(checkid != 0) for(i=0; inarrays; i++) free(q->arrays[i]); if(q->narrays > 0) { free(q->array_sizes); free(q->arrays); } free(q); NGENS--; return NGENS; } #ifdef __STDC__ int pack_rng( int *genptr, char **buffer) #else int pack_rng(genptr,buffer) int *genptr; char **buffer; #endif { unsigned char *p, *initp; int size, i; unsigned int temp, m[2]; struct rngen *q; q = (struct rngen *) genptr; size = 64 + strlen(q->gentype)+1; initp = p = (unsigned char *) mymalloc(size); /* allocate memory */ /* The new load/store routines make using sizeof unnecessary. Infact, */ /* using sizeof could be erroneous. */ if(p == NULL) { *buffer = NULL; return 0; } strcpy((char *)p,q->gentype); p += strlen(q->gentype)+1; p += store_int(q->stream_number,4,p); p += store_int(q->nstreams,4,p); p += store_int(q->init_seed,4,p); p += store_int(q->parameter,4,p); p += store_int(q->narrays,4,p); p += store_int(q->spawn_offset,4,p); p += store_int(q->prime,4,p); #ifdef LONG64 /* 64 bit integer types */ p += store_long64(q->state,8,p); p += store_long64(q->multiplier,8,p); p += store_long64(q->s0,4,p); p += store_long64(q->s1,4,p); p += store_long64(q->s2,4,p); p += store_long64(q->s3,4,p); p += store_long64(q->s4,4,p); #else /* No 64 bit type available */ m[0] = q->state[2]; temp = q->state[1];m[0]=(m[0]<<12)|(temp>>10); m[1] = q->state[1]; temp = q->state[0];m[1]=(m[1]<<22)|(temp); p += store_intarray(m,2,4,p); m[0] = q->multiplier[2]; temp = q->multiplier[1];m[0]=(m[0]<<12)|(temp>>10); m[1] = q->multiplier[1]; temp = q->multiplier[0];m[1]=(m[1]<<22)|(temp); p += store_intarray(m,2,4,p); p += store_int(*(unsigned int *)&q->s0,4,p); p += store_int(*(unsigned int *)&q->s1,4,p); p += store_int(*(unsigned int *)&q->s2,4,p); p += store_int(*(unsigned int *)&q->s3,4,p); p += store_int(*(unsigned int *)&q->s4,4,p); #endif *buffer = (char *) initp; assert(p-initp == size); return p-initp; } #ifdef __STDC__ int *unpack_rng( char *packed) #else int *unpack_rng(packed) char *packed; #endif { struct rngen *q; unsigned int i, m[2]; unsigned char *p; p = (unsigned char *) packed; q = (struct rngen *) mymalloc(sizeof(struct rngen)); if(q == NULL) return NULL; if(strcmp((char *)p,GENTYPE) != 0) { fprintf(stderr,"ERROR: Unpacked ' %.24s ' instead of ' %s '\n", p, GENTYPE); return NULL; } else q->gentype = GENTYPE; p += strlen(q->gentype)+1; p += load_int(p,4,(unsigned int *)&q->stream_number); p += load_int(p,4,(unsigned int *)&q->nstreams); p += load_int(p,4,(unsigned int *)&q->init_seed); p += load_int(p,4,(unsigned int *)&q->parameter); p += load_int(p,4,(unsigned int *)&q->narrays); p += load_int(p,4,(unsigned int *)&q->spawn_offset); p += load_int(p,4,&q->prime); #ifdef LONG64 /* 64 bit integer types */ p += load_long64(p,8,&q->state); p += load_long64(p,8,&q->multiplier); p += load_long64(p,4,&q->s0); p += load_long64(p,4,&q->s1); p += load_long64(p,4,&q->s2); p += load_long64(p,4,&q->s3); p += load_long64(p,4,&q->s4); #else /* No 64 bit type available */ p += load_intarray(p,2,4,m); q->state[0] = (double) (m[1]&0x3fffff); q->state[1] = (double) ((m[1]>>22) | (m[0]&0xfff)<<10); q->state[2] = (double) (m[0]>>12); p += load_intarray(p,2,4,m); q->multiplier[0] = (double) (m[1]&0x3fffff); q->multiplier[1] = (double) ((m[1]>>22) | (m[0]&0xfff)<<10); q->multiplier[2] = (double) (m[0]>>12); p += load_int(p,4,(unsigned int *)&q->s0); p += load_int(p,4,(unsigned int *)&q->s1); p += load_int(p,4,(unsigned int *)&q->s2); p += load_int(p,4,(unsigned int *)&q->s3); p += load_int(p,4,(unsigned int *)&q->s4); #endif q->array_sizes = NULL; q->arrays = NULL; NGENS++; return (int *) q; } #ifdef __STDC__ int get_seed_rng(int *gen) #else int get_seed_rng(gen) int *gen; #endif { return ((struct rngen *) gen)->init_seed; } #ifdef __STDC__ int print_rng( int *igen) #else int print_rng(igen) int *igen; #endif { struct rngen *gen; printf("\n%s\n", GENTYPE+2); gen = (struct rngen *) igen; printf("\n \tseed = %d, stream_number = %d\tparameter = %d\n\n", gen->init_seed, gen->stream_number, gen->parameter); return 1; } /* HAS ;-) */ #if 0 #include "simple_.h" #include "../fwrap_.h" #endif tree-puzzle-5.2/src/sprng/Makefile.am0000644000076400001440000000321310073365177013313 # # Makefile.am for SPRNG 1.0 # SPRNG itself is written by Mascagni and Srinivasan (2000) # # # Part of TREE-PUZZLE 5.2 (July 2004) # # (c) 2003-2004 by Heiko A. 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The intent in sharing */ /* this software is to promote the productive interchange of ideas */ /* throughout the research community. All software is furnished on an */ /* "as is" basis. No further updates to this software should be */ /* expected. Although this may occur, no commitment exists. The authors */ /* certainly invite your comments as well as the reporting of any bugs. */ /* NCSA cannot commit that any or all bugs will be fixed. */ /*************************************************************************/ /*************************************************************************/ /* This is version 0.2, created 26 Dec 1997 */ #include #include #include #define NDEBUG #include #include "memory.h" #include "interface.h" #include "int64.h" #define VERSION "00" /*** Name for Generator ***/ #define GENTYPE VERSION "Multiplicative Lagged Fibonacci Generator" #define NPARAMS 11 /* number of valid parameters */ int MAX_STREAMS = 0x7fffffff; /* Maximum number streams to init_sprng */ struct rngen { char *gentype; int stream_number; int nstreams; int init_seed; int parameter; int narrays; int *array_sizes; int **arrays; uint64 *lags; uint64 *si; int hptr; /* integer pointer into fill */ int lval, kval, seed; }; struct vstruct { int L; int K; int LSBS; /* number of least significant bits that are 1 */ int first; /* the first seed whose LSB is 1 */ }; const struct vstruct valid[] = { {17,5,1,10}, {31,6,1,2}, {55,24,1,11}, {63,31,1,14}, {127,97,1,21}, {521,353,1,100}, {521,168,1,83}, {607,334,1,166}, {607,273,1,105}, {1279,418,1,208}, {1279,861,1,233} }; #define TWO_M52 2.2204460492503131e-16 /* 2^(-52) */ #define TWO_M64 5.4210108624275222e-20 /* 2^(-64) */ #define BITS 62 /* Initialization of ALFG part is m-2 bits */ #define MAX_BIT_INT (BITS-2) #define RUNUP (2*BITS) /* Do RUNUP iterations after initialization */ #define GS0 0x372f05ac #ifdef LONG64 #define INT_MOD_MASK (MASK64>>(64-BITS)) #define INT_MASK (MASK64>>(64-BITS+1)) #define INTX2_MASK ((((uint64)1)<=0;i--) { new_fill[0] = (new_fill[0]<<1) | (1&bitcnt(reg_fill[0]&temp)); new_fill[1] = (new_fill[1]<<1) | (1&bitcnt(reg_fill[1]&temp)); temp >>= 1; } for (i=28;i<32;i++) { temp = bitcnt(reg_fill[0]&(mask<>(32-i))); new_fill[0] |= (1&temp)<=0;i--) { and(b[i],mask1,temp1) if(notzero(temp1)) add(a[i+1],ONE,a[i+1]); and(b[i],INTX2_MASK,temp1); lshift(temp1,1,a[i]); } } static void pow3(uint64 n, uint64 *ui) /* return 3^n (mod 2^BITS) */ { uint64 p, value, temp, bit, temp2, temp3; int exponent; set(n,p); seti(3,temp); seti(1,temp3); and(n,temp3,temp2); if(notzero(temp2)) seti(3,value) else seti(1,value) seti(1,bit); for(exponent=2; exponent<64; exponent++) { multiply(temp,temp,temp); lshift(bit,1,bit); and(bit,n,temp2); if(notzero(temp2)) multiply(value,temp,value); } and(value,MASK64,value); set(value,(*ui)); } static void findseed(int sign, uint64 n, uint64 *ui) { uint64 temp; pow3(n,&temp); if(sign&1) multiply(temp,MINUS1,temp); set(temp,(*ui)); } #define advance_state(genptr) {int lval = genptr->lval, kval = genptr->kval;\ int lptr;\ genptr->hptr--;\ if(genptr->hptr < 0)\ genptr->hptr = lval-1;\ lptr = genptr->hptr + kval;\ if (lptr>=lval)\ lptr -= lval;\ multiply(genptr->lags[genptr->hptr],genptr->lags[lptr],genptr->lags[genptr->hptr]);} static struct rngen **initialize(int ngen, int param, unsigned int seed, uint64 *nstart, unsigned int initseed) { int i,j,k,l,m,*order, length; struct rngen **q; uint64 *nindex, temp1, mask; length = valid[param].L; order = (int *) mymalloc(ngen*sizeof(int)); q = (struct rngen **) mymalloc(ngen*sizeof(struct rngen *)); if (q == NULL || order == NULL) return NULL; for (i=0;ihptr = 0; /* This is reset to lval-1 before first iteration */ q[i]->si = (uint64 *) mymalloc((length-1)*sizeof(uint64)); q[i]->lags = (uint64 *) mymalloc(length*sizeof(uint64)); q[i]->lval = length; q[i]->kval = valid[param].K; q[i]->parameter = param; q[i]->seed = seed; q[i]->init_seed = initseed; q[i]->narrays=2; q[i]->gentype = GENTYPE; if (q[i]->lags == NULL || q[i]->si == NULL) return NULL; } /* specify register fills and node number arrays */ /* do fills in tree fashion so that all fills branch from index */ /* contained in nstart array */ q[0]->stream_number = lowword(nstart[0]); get_fill(nstart,q[0]->lags,param,seed); si_double(q[0]->si,nstart,length); set(ONE,mask); for(m=0; mlags[m], &q[0]->lags[m]); else findseed(0,q[0]->lags[m], &q[0]->lags[m]); lshift(mask,1,mask); } add(q[0]->si[0],ONE,q[0]->si[0]); i = 1; order[0] = 0; if (ngen>1) while (1) { l = i; for (k=0;ksi; q[i]->stream_number = lowword(nindex[0]); get_fill(nindex,q[i]->lags,param,seed); si_double(nindex,nindex, length); for (j=0;jsi[j]); set(ONE,mask); for(m=0; mlags[m], &q[i]->lags[m]); else findseed(0,q[i]->lags[m], &q[i]->lags[m]); lshift(mask,1,mask); } add(q[i]->si[0],ONE,q[i]->si[0]); if (ngen == ++i) break; } if (ngen == i) break; for (k=l-1;k>0;k--) { order[2*k+1] = l+k; order[2*k] = order[k]; } order[1] = l; } free(order); for (i=ngen-1;i>=0;i--) { k = 0; for (j=1;jsi[j])) k = 1; if (!k) break; for (j=0;j=0) { for (j=0;j<4*length;j++) advance_state(q[i]); i--; } return q; } /* Initialize random number stream */ #ifdef __STDC__ int *init_rng( int gennum, int total_gen, int seed, int param) #else int *init_rng(gennum,total_gen,seed,param) int gennum,param,seed,total_gen; #endif { /* gives back one stream (node gennum) with updated spawning */ /* info; should be called total_gen times, with different value */ /* of gennum in [0,total_gen) each call */ struct rngen **p=NULL, *genptr; uint64 *nstart=NULL,*si; int i, length, k; if (total_gen <= 0) /* Is total_gen valid ? */ { total_gen = 1; fprintf(stderr,"WARNING - init_rng: Total_gen <= 0. Default value of 1 used for total_gen\n"); } if (gennum >= MAX_STREAMS) /* check if gen_num is valid */ fprintf(stderr,"WARNING - init_rng: gennum: %d > maximum number of independent streams: %d\n\tIndependence of streams cannot be guranteed.\n", gennum, MAX_STREAMS); if (gennum < 0 || gennum >= total_gen) /* check if gen_num is valid */ { fprintf(stderr,"ERROR - init_rng: gennum %d out of range [%d,%d).\n", gennum, 0, total_gen); return (int *) NULL; } seed &= 0x7fffffff; /* Only 31 LSB of seed considered */ if (param < 0 || param >= NPARAMS) /* check if parameter is valid */ { fprintf(stderr,"WARNING - init_rng: parameter not valid. Using Default parameter.\n"); param = 0; } length = valid[param].L; /* determine parameters */ k = valid[param].K; /* define the starting vector for the initial node */ nstart = (uint64 *) mymalloc((length-1)*sizeof(uint64)); if (nstart == NULL) return NULL; seti(gennum,nstart[0]); for (i=1;isi; while (lowword(si[0]) < total_gen && !highword(si[0])) si_double(si,si,length); NGENS++; genptr->stream_number = gennum; genptr->nstreams = total_gen; genptr->array_sizes = (int *) mymalloc(genptr->narrays*sizeof(int)); genptr->arrays = (int **) mymalloc(genptr->narrays*sizeof(int *)); if(genptr->array_sizes == NULL || genptr->arrays == NULL) return NULL; genptr->arrays[0] = (int *) genptr->lags; genptr->arrays[1] = (int *) genptr->si; genptr->array_sizes[0] = genptr->lval*sizeof(uint64)/sizeof(int); genptr->array_sizes[1] = (genptr->lval-1)*sizeof(uint64)/sizeof(int); return (int *) genptr; } /* Returns a double precision random number */ #ifdef __STDC__ double get_rn_dbl(int *igenptr) #else double get_rn_dbl(igenptr) int *igenptr; #endif { struct rngen *genptr = (struct rngen *) igenptr; advance_state(genptr); /*printf("\t sprng: %lu\n", genptr->lags[genptr->hptr]);*/ #ifdef LONG64 return (genptr->lags[genptr->hptr]>>12)*TWO_M52; #else return (genptr->lags[genptr->hptr][1])*TWO_M32 + (genptr->lags[genptr->hptr][0])*TWO_M64; #endif } /* Return a random integer */ #ifdef __STDC__ int get_rn_int(int *igenptr) #else int get_rn_int(igenptr) int *igenptr; #endif { struct rngen *genptr = (struct rngen *) igenptr; advance_state(genptr); #ifdef LONG64 return genptr->lags[genptr->hptr]>>33; #else return genptr->lags[genptr->hptr][1]>>1; #endif } /* Return a single precision random number */ #ifdef __STDC__ float get_rn_flt(int *igenptr) #else float get_rn_flt(igenptr) int *igenptr; #endif { /* If you have a more efficient way of computing the random integer, then please replace the statement below with your scheme. */ return (float) get_rn_dbl(igenptr); } /*************************************************************************/ /*************************************************************************/ /* SPAWN_RNG: spawns new generators */ /*************************************************************************/ /*************************************************************************/ #ifdef __STDC__ int spawn_rng(int *igenptr, int nspawned, int ***newgens, int checkid) #else int spawn_rng(igenptr,nspawned, newgens, checkid) int *igenptr,nspawned, ***newgens, checkid; #endif { struct rngen **genptr, *temp = (struct rngen *) igenptr; int i; uint64 *p; if (nspawned <= 0) /* is nspawned valid ? */ { nspawned = 1; fprintf(stderr,"WARNING - spawn_rng: nspawned <= 0. Default value of 1 used for nspawned\n"); } p = temp->si; genptr = initialize(nspawned,temp->parameter,temp->seed,p,temp->init_seed); if(genptr == NULL) /* allocate memory for pointers to structures */ { *newgens = NULL; return 0; } si_double(p,p,temp->lval); for(i=0; iarray_sizes = (int *) mymalloc(genptr[i]->narrays*sizeof(int)); genptr[i]->arrays = (int **) mymalloc(genptr[i]->narrays*sizeof(int *)); if(genptr[i]->array_sizes == NULL || genptr[i]->arrays == NULL) return 0; genptr[i]->arrays[0] = (int *) genptr[i]->lags; genptr[i]->arrays[1] = (int *) genptr[i]->si; genptr[i]->array_sizes[0] = genptr[i]->lval*sizeof(uint64)/sizeof(int); genptr[i]->array_sizes[1] = (genptr[i]->lval-1)*sizeof(uint64)/sizeof(int); } NGENS += nspawned; *newgens = (int **) genptr; if(checkid != 0) for(i=0; inarrays; i++) free(q->arrays[i]); if(q->narrays > 0) { free(q->array_sizes); free(q->arrays); } free(q); NGENS--; return NGENS; } #ifdef __STDC__ int pack_rng( int *genptr, char **buffer) #else int pack_rng(genptr,buffer) int *genptr; char **buffer; #endif { unsigned char *p, *initp; int size, i; struct rngen *q; q = (struct rngen *) genptr; size = 24+16*q->lval + strlen(q->gentype)+1; initp = p = (unsigned char *) mymalloc(size); /* allocate memory */ if(p == NULL) { *buffer = NULL; return 0; } strcpy((char *) p,q->gentype); p += strlen(q->gentype)+1; p += store_int(q->stream_number,4,p); p += store_int(q->nstreams,4,p); p += store_int(q->init_seed,4,p); p += store_int(q->parameter,4,p); p += store_int(q->hptr,4,p); p += store_int(q->lval,4,p); p += store_int(q->kval,4,p); p += store_int(q->seed,4,p); p += store_uint64array(q->si,q->lval-1,p); p += store_uint64array(q->lags,q->lval,p); *buffer = (char *) initp; assert(p-initp == size); return p-initp; } #ifdef __STDC__ int *unpack_rng( char *packed) #else int *unpack_rng(packed) char *packed; #endif { struct rngen *q; unsigned char *p; int i, found; q = (struct rngen *) mymalloc(sizeof(struct rngen)); if(q == NULL) return NULL; p = (unsigned char *) packed; if(strcmp((char *) p,GENTYPE) != 0) { fprintf(stderr,"ERROR: Unpacked ' %.24s ' instead of ' %s '\n", p, GENTYPE); return NULL; } else q->gentype = GENTYPE; p += strlen(q->gentype)+1; p += load_int(p,4,(unsigned int *)&q->stream_number); p += load_int(p,4,(unsigned int *)&q->nstreams); p += load_int(p,4,(unsigned int *)&q->init_seed); p += load_int(p,4,(unsigned int *)&q->parameter); p += load_int(p,4,(unsigned int *)&q->hptr); p += load_int(p,4,(unsigned int *)&q->lval); p += load_int(p,4,(unsigned int *)&q->kval); p += load_int(p,4,(unsigned int *)&q->seed); /* check values of parameters for consistency */ for(i=found=0; ilval==valid[i].L && q->kval==valid[i].K) { found = 1; break; } if(found == 0) { fprintf(stderr,"ERROR: Unpacked parameters are not acceptable.\n"); return NULL; } q->narrays = 2; q->array_sizes = (int *) mymalloc(q->narrays*sizeof(int)); q->arrays = (int **) mymalloc(q->narrays*sizeof(int *)); if(q->array_sizes == NULL || q->arrays == NULL) return NULL; q->array_sizes[0] = q->lval*sizeof(uint64)/sizeof(int); q->array_sizes[1] = (q->lval-1)*sizeof(uint64)/sizeof(int); for(i=0; inarrays; i++) { q->arrays[i] = (int *) mymalloc(q->array_sizes[i]*sizeof(int)); if(q->arrays[i] == NULL) return NULL; } q->lags = (uint64 *) q->arrays[0]; q->si = (uint64 *) q->arrays[1]; p += load_uint64array(p,q->lval-1,q->si); p += load_uint64array(p,q->lval,q->lags); NGENS++; return (int *) q; } #ifdef __STDC__ int get_seed_rng(int *gen) #else int get_seed_rng(gen) int *gen; #endif { return ((struct rngen *) gen)->init_seed; } #ifdef __STDC__ int print_rng( int *igen) #else int print_rng(igen) int *igen; #endif { struct rngen *gen; printf("\n%s\n", GENTYPE+2); gen = (struct rngen *) igen; printf("\n \tseed = %d, stream_number = %d\tparameter = %d\n\n", gen->init_seed, gen->stream_number, gen->parameter); return 1; } /* HAS ;-) */ #if 0 #include "simple_.h" #include "../fwrap_.h" #endif tree-puzzle-5.2/src/sprng/communicate.c0000644000076400001440000000175207754754335013747 #ifdef SPRNG_MPI #include #endif /* SPRNG_MPI */ #include #include "interface.h" #ifdef __STDC__ void get_proc_info_mpi(int *myid, int *nprocs) #else void get_proc_info_mpi(myid, nprocs) int *myid, *nprocs; #endif { #ifdef SPRNG_MPI MPI_Comm_rank(MPI_COMM_WORLD, myid); MPI_Comm_size(MPI_COMM_WORLD, nprocs); #else *myid = 0; *nprocs = 1; #endif } #ifdef __STDC__ int make_new_seed_mpi(void) #else int make_new_seed_mpi() #endif { #ifdef SPRNG_MPI unsigned int temp2; int myid, nprocs; MPI_Comm newcomm; MPI_Comm_dup(MPI_COMM_WORLD, &newcomm); /* create a temporary communicator */ MPI_Comm_rank(newcomm, &myid); MPI_Comm_size(newcomm, &nprocs); if(myid == 0) temp2 = make_new_seed(); MPI_Bcast(&temp2,1,MPI_UNSIGNED,0,newcomm); MPI_Comm_free(&newcomm); return temp2; #else return make_new_seed(); #endif } /* HAS ;-) */ #ifdef SPRNG_MPI_TEST main() { printf("%u\n", make_new_seed()); printf("%u\n", make_new_seed()); } #endif tree-puzzle-5.2/src/sprng/checkid.c0000644000076400001440000000351007756435656013033 #include #include #include "memory.h" #define CHECK_MASK 0x1c /* Assumes exactly last two bits are 0 ... */ /* ... If not, change checklist dimension */ typedef struct checkidstruct { int *ID; struct checkidstruct *next; } Checklisttype; Checklisttype checklist[(CHECK_MASK>>2)+1] = {{NULL,NULL},{NULL,NULL},{NULL,NULL},{NULL,NULL}}; #ifdef __STDC__ int *checkID( int *ptr) #else int *checkID(ptr) int *ptr; #endif { int bucket; Checklisttype *next; if(ptr == NULL) return NULL; bucket = (((long) ptr)&CHECK_MASK)>>2; next = checklist[bucket].next; while(next != NULL) { if(next->ID == ptr) { return (int *) ptr; } else { next = next->next; } } fprintf(stderr,"ERROR: Invalid generator ID %p\n", ptr); return NULL; } #ifdef __STDC__ int *deleteID( int *ptr) #else int *deleteID(ptr) int *ptr; #endif { int bucket; Checklisttype *next, *temp; if(ptr == NULL) return NULL; bucket = (((long) ptr)&CHECK_MASK)>>2; next = &checklist[bucket]; while(next->next != NULL) if(next->next->ID == ptr) { temp = next->next; next->next = next->next->next; free(temp); return (int *) ptr; } else { next = next->next; } fprintf(stderr,"ERROR: Invalid generator ID %p\n", ptr); return NULL; } #ifdef __STDC__ int *addID( int *ptr) #else int *addID(ptr) int *ptr; #endif { int bucket; Checklisttype *next, *temp; if(ptr == NULL) return NULL; bucket = (((long) ptr)&CHECK_MASK)>>2; temp = (Checklisttype *) mymalloc(sizeof(Checklisttype)); if(temp == NULL) return NULL; temp->ID = (int *) ptr; temp->next = checklist[bucket].next; checklist[bucket].next = temp; return (int *) ptr; } tree-puzzle-5.2/src/sprng/int64.h0000644000076400001440000000760207755111260012375 #ifndef _INT64_H_ #define _INT64_H_ /* used by mlfg */ #include #include "store.h" #ifndef __STDC__ #define const /* old C does not have 'const' qualifier */ #endif #if LONG_MAX > 2147483647L #if LONG_MAX > 35184372088831L #if LONG_MAX >= 9223372036854775807L #define LONG_SPRNG #define LONG64 long /* 64 bit long */ #endif #endif #endif #if !defined(LONG_SPRNG) && defined(_LONG_LONG) #define LONG64 long long #endif #ifdef LONG64 typedef unsigned LONG64 uint64; #ifdef LONG_SPRNG #define MINUS1 0xffffffffffffffffUL /* -1 (mod 2^(BITS-2)) */ #define ONE 0x1UL #define MASK64 0xffffffffffffffffUL #else #define MINUS1 0xffffffffffffffffULL /* -1 (mod 2^(BITS-2)) */ #define ONE 0x1ULL #define MASK64 0xffffffffffffffffULL #endif #define multiply(a,b,c) {c = (a)*(b); c &= MASK64;} #define add(a,b,c) {c = (a)+(b); c &= MASK64;} #define decrement(a,c) {c = (a)-1; c &= MASK64;} #define and(a,b,c) {c = (a)&(b);} #define or(a,b,c) {c = (a)|(b);} #define xor(a,b,c) {c = (a)^(b);} #define notzero(a) (a==0?0:1) #define lshift(a,b,c) {c = (a)<<(b); c &= MASK64;} /* b is an int */ #define rshift(a,b,c) {c = (a)>>(b); c &= MASK64;} /* b is an int */ #define highword(a) ((unsigned int)((a)>>32)) #define lowword(a) ((unsigned int)((a)&0xffffffff)) #define set(a,b) {b = (a)&MASK64;} #define seti(a,b) {b = (a)&MASK64;} /* b is an int */ #define seti2(a,b,c) {c = (b); c <<= 32; c |= (a); c &= MASK64;}/*a,b=+int*/ #else /* Simulate 64 bit arithmetic on 32 bit integers */ typedef unsigned int uint64[2]; static const uint64 MASK64={0xffffffffU,0xffffffffU}; static const uint64 MINUS1={0xffffffffU,0xffffffffU}; /* -1 (mod 2^(BITS-2)) */ static uint64 ONE={0x1U,0x0U}; #define TWO_M32 2.3283064365386962e-10 /* 2^(-32) */ #define and(a,b,c) {c[0] = a[0]&b[0]; c[1] = a[1]&b[1];} #define or(a,b,c) {c[0] = a[0]|b[0]; c[1] = a[1]|b[1];} #define xor(a,b,c) {c[0] = a[0]^b[0]; c[1] = a[1]^b[1];} #define notzero(a) ((a[0]==0 && a[1]==0)?0:1) #define multiply(a,b,c) {c[1] = a[0]*b[1]+a[1]*b[0];\ c[1] += (unsigned int) (((double)a[0]*(double)b[0])\ *TWO_M32);\ c[0] = a[0]*b[0]; and(c,MASK64,c);} #define add(a,b,c) {unsigned int t = a[0]+b[0]; \ c[1] = a[1]+b[1]+(t>(32-b)); c[0] = a[0]<<(b);} else {c[1]=a[0]<<(b-32);c[0]=0;} and(c,MASK64,c); } static void rshift(uint64 a,int b,uint64 c) { if(b<32) {c[0] = (a[0]>>b)|(a[1]<<(32-b));c[1] = a[1]>>(b);} else {c[0]=a[1]>>(b-32);c[1]=0;} and(c,MASK64,c); } #define highword(a) ((a)[1]) #define lowword(a) ((a)[0]) #define set(a,b) {b[0] = a[0];b[1]=a[1];and(b,MASK64,b);} #define seti(a,b) {b[0] = a;b[1]=0;} /* b is an int */ #define seti2(a,b,c) {c[1] = b; c[0] = a; and(c,MASK64,c);}/*a,b = +ve int*/ #endif /* LONG64 or 32 bit */ static int store_uint64(uint64 l, unsigned char *c) { int i; unsigned int m[2]; m[0] = highword(l); m[1] = lowword(l); c += store_intarray(m,2,4,c); return 8; /* return number of chars filled */ } static int store_uint64array(uint64 *l, int n, unsigned char *c) { int i; for(i=0; i #include #ifdef __STDC__ void *_mymalloc(long size, int line, char *message) #else void *_mymalloc(size, line, message) long size; int line; char *message; #endif { char *temp; if(size == 0) return NULL; temp = (char *) malloc(size); if(temp == NULL) { fprintf(stderr,"\nmemory allocation failure in file: %s at line number: %d\n", message, line); return NULL; } return (void *) temp; } tree-puzzle-5.2/src/sprng/memory.h0000644000076400001440000000035307754747713012756 #define mymalloc(a) (_mymalloc((a), __LINE__, __FILE__)) #ifndef ANSI_ARGS #ifdef __STDC__ #define ANSI_ARGS(args) args #else #define ANSI_ARGS(args) () #endif #endif void *_mymalloc ANSI_ARGS((long size, int line, char *message)); tree-puzzle-5.2/src/treesort.c0000644000076400001440000005141410073365205012137 /* * treesort.c * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #define EXTERN extern #include "treesort.h" int YYY=0; /* fprintf(stderr, "YYY: %d (%s:%d)\n", YYY++, __FILE__, __LINE__); */ /*******************************************/ /* tree sorting */ /*******************************************/ /* compute address of the 4 int (sort key) in the 4 int node */ int ct_sortkeyaddr(int addr) { int a, res; a = addr % 4; res = addr - a + 3; return res; } /* ct_sortkeyaddr */ /**********/ /* compute address of the next edge pointer in a 4 int node (0->1->2->0) */ int ct_nextedgeaddr(int addr) { int a, res; a = addr % 4; if ( a == 2 ) { res = addr - 2; } else { res = addr + 1; } return res; } /* ct_nextedgeaddr */ /**********/ /* compute address of 1st edge of a 4 int node from node number */ int ct_1stedge(int node) { int res; res = 4 * node; return res; } /* ct_1stedge */ /**********/ /* compute address of 2nd edge of a 4 int node from node number */ int ct_2ndedge(int node) { int res; res = 4 * node +1; return res; } /* ct_2ndedge */ /**********/ /* compute address of 3rd edge of a 4 int node from node number */ int ct_3rdedge(int node) { int res; res = 4 * node +2; return res; } /* ct_3rdedge */ /**********/ /* check whether node 'node' is a leaf (2nd/3rd edge pointer = -1) */ int ct_isleaf(int node, int *ctree) { return (ctree[ct_3rdedge(node)] < 0); } /* ct_isleaf */ /**********/ /* compute node number of 4 int node from an edge addr. */ int ct_addr2node(int addr) { int a, res; a = addr % 4; res = (int) ((addr - a) / 4); return res; } /* ct_addr2node */ /**********/ /* print graph pointers for checking */ void printctree(int *ctree) { int n; for (n=0; n < 2*Maxspc; n++) { printf("n[%3d] = (%3d.%2d, %3d.%2d, %3d.%2d | %3d)\n", n, (int) ctree[ct_1stedge(n)]/4, (int) ctree[ct_1stedge(n)]%4, (int) ctree[ct_2ndedge(n)]/4, (int) ctree[ct_2ndedge(n)]%4, (int) ctree[ct_3rdedge(n)]/4, (int) ctree[ct_3rdedge(n)]%4, ctree[ct_3rdedge(n)+1]); } printf("\n"); } /* printctree */ /**********/ /* allocate memory for ctree 3 ints pointer plus 1 check byte */ int *initctree(void) { int *snodes; int n; snodes = (int *) calloc((size_t) (4 * 2 * Maxspc), sizeof(int)); if (snodes == NULL) maerror("snodes in copytree"); for (n=0; n<(4 * 2 * Maxspc); n++) { snodes[n]=-1; } return snodes; } /* initctree */ /**********/ /* free memory of a tree for sorting */ void freectree(int **snodes) { free(*snodes); *snodes = NULL; } /* freectree */ #if 0 /**********/ /* trueID (HAS) */ /* copy subtree recursively */ void copyOTU_trueID(int *ctree, /* in/out: tree array struct */ int *ct_nextnode,/* in/out: next free node */ int ct_curredge,/* in: currend edge to add subtree */ int *ct_nextleaf,/* in/out: next free leaf (0-maxspc) */ int ed, /* in: current edge in puzzling tree */ ONEEDGE *edge, /* in: tree topology */ int *edgeofleaf, /* in: external edge list */ int numleaves, /* in: number of leaves */ int *trueID) /* in: permutation vector */ { int i, nextcurredge; /* test whether we are on a leaf */ if (edge[ed].downright == NULL && edge[ed].downleft == NULL) { for (i = 1; i < numleaves; i++) { if (edgeofleaf[i] == ed) { /* i is the leaf of ed */ nextcurredge = ct_1stedge(*ct_nextleaf); ctree[ct_curredge] = nextcurredge; ctree[nextcurredge] = ct_curredge; /* trueID (HAS) */ ctree[ct_sortkeyaddr(nextcurredge)] = trueID[i]; (*ct_nextleaf)++; return; } } } /* we are NOT on a leaf */ nextcurredge = ct_1stedge(*ct_nextnode); ctree[ct_curredge] = nextcurredge; ctree[nextcurredge] = ct_curredge; (*ct_nextnode)++; nextcurredge = ct_nextedgeaddr(nextcurredge); copyOTU_trueID(ctree, ct_nextnode, nextcurredge, ct_nextleaf, edge[ed].downleft->numedge, edge, edgeofleaf, numleaves, trueID); nextcurredge = ct_nextedgeaddr(nextcurredge); copyOTU_trueID(ctree, ct_nextnode, nextcurredge, ct_nextleaf, edge[ed].downright->numedge, edge, edgeofleaf, numleaves, trueID); } /* copyOTU_trueID */ /********/ /* trueID (HAS) */ /* copy treestructure to sorting structure */ void copytree_trueID(int *ctree, /* out: copy for effective sorting */ int *trueID, /* in: permutation vector */ ONEEDGE *edgeset, /* in: intermediate tree topology */ int *edgeofleaf, /* dito. */ int numleaves) /* in: number of leaves */ { int ct_curredge; int ct_nextleaf; int ct_nextnode; ct_nextnode = Maxspc; ct_curredge = ct_1stedge(ct_nextnode); ct_nextleaf = 1; ctree[ct_1stedge(0)] = ct_curredge; ctree[ct_curredge] = ct_1stedge(0); /* trueID (HAS) */ ctree[ct_sortkeyaddr(0)] = trueID[0]; ct_nextnode++; ct_curredge = ct_nextedgeaddr(ct_curredge); copyOTU_trueID(ctree, &ct_nextnode, ct_curredge, &ct_nextleaf, edgeset[edgeofleaf[0]].downleft->numedge, edgeset, edgeofleaf, numleaves, trueID); ct_curredge = ct_nextedgeaddr(ct_curredge); copyOTU_trueID(ctree, &ct_nextnode, ct_curredge, &ct_nextleaf, edgeset[edgeofleaf[0]].downright->numedge, edgeset, edgeofleaf, numleaves, trueID); } /* copytree_trueID */ #endif /**********/ /* copy subtree recursively */ void copyOTU(int *ctree, /* in/out: tree array struct */ int *ct_nextnode,/* in/out: next free node */ int ct_curredge,/* in: currend edge to add subtree */ int *ct_nextleaf,/* in/out: next free leaf (0-maxspc) */ int ed, /* in: current edge in puzzling tree */ ONEEDGE *edge, /* in: tree topology */ int *edgeofleaf, /* in: external edge list */ int numleaves) /* in: number of leaves */ { int nextcurredge; /* test whether we are on a leaf */ if (edge[ed].downright == NULL && edge[ed].downleft == NULL) { nextcurredge = ct_1stedge(*ct_nextleaf); ctree[ct_curredge] = nextcurredge; ctree[nextcurredge] = ct_curredge; ctree[ct_sortkeyaddr(nextcurredge)] = edge[ed].taxon; (*ct_nextleaf)++; return; } /* we are NOT on a leaf */ nextcurredge = ct_1stedge(*ct_nextnode); ctree[ct_curredge] = nextcurredge; ctree[nextcurredge] = ct_curredge; (*ct_nextnode)++; nextcurredge = ct_nextedgeaddr(nextcurredge); copyOTU(ctree, ct_nextnode, nextcurredge, ct_nextleaf, edge[ed].downleft->numedge, edge, edgeofleaf, numleaves); nextcurredge = ct_nextedgeaddr(nextcurredge); copyOTU(ctree, ct_nextnode, nextcurredge, ct_nextleaf, edge[ed].downright->numedge, edge, edgeofleaf, numleaves); } /* copyOTU */ /**********/ /* copy treestructure to sorting structure */ void copytree(int *ctree, /* out: copy for effective sorting */ ONEEDGE *edgeset, /* in: intermediate tree topology */ int *edgeofleaf, /* dito. */ int rootleaf, int numleaves) /* in: number of leaves */ { int ct_curredge; int ct_nextleaf; int ct_nextnode; ct_nextnode = Maxspc; ct_curredge = ct_1stedge(ct_nextnode); ct_nextleaf = 1; ctree[ct_1stedge(0)] = ct_curredge; ctree[ct_curredge] = ct_1stedge(0); ctree[ct_sortkeyaddr(0)] = rootleaf; ct_nextnode++; ct_curredge = ct_nextedgeaddr(ct_curredge); copyOTU(ctree, &ct_nextnode, ct_curredge, &ct_nextleaf, edgeset[edgeofleaf[rootleaf]].downleft->numedge, edgeset, edgeofleaf, numleaves); ct_curredge = ct_nextedgeaddr(ct_curredge); copyOTU(ctree, &ct_nextnode, ct_curredge, &ct_nextleaf, edgeset[edgeofleaf[rootleaf]].downright->numedge, edgeset, edgeofleaf, numleaves); } /* copytree */ /**********/ /* sort subtree from edge recursively by indices */ int sortOTU(int edge, int *ctree) { int key1, key2; int edge1, edge2; int tempedge; /* if leaf, return taxonID */ if (ctree[ct_2ndedge((int) (edge / 4))] < 0) return ctree[ct_sortkeyaddr(edge)]; edge1 = ctree[ct_nextedgeaddr(edge)]; edge2 = ctree[ct_nextedgeaddr(ct_nextedgeaddr(edge))]; /* printf ("visiting [%5d] -> [%5d], [%5d]\n", edge, edge1, edge2); */ /* printf ("visiting [%2d.%2d] -> [%2d.%2d], [%2d.%2d]\n", (int)(edge/4), edge%4, (int)(edge1/4), edge1%4, (int)(edge2/4), edge2%4); */ key1 = sortOTU(edge1, ctree); key2 = sortOTU(edge2, ctree); if (key2 < key1) { tempedge = ctree[ctree[edge1]]; ctree[ctree[edge1]] = ctree[ctree[edge2]]; ctree[ctree[edge2]] = tempedge; tempedge = ctree[edge1]; ctree[edge1] = ctree[edge2]; ctree[edge2] = tempedge; ctree[ct_sortkeyaddr(edge)] = key2; } else { ctree[ct_sortkeyaddr(edge)] = key1; } return ctree[ct_sortkeyaddr(edge)]; } /* sortOTU */ /**********/ /* sort ctree recursively by indices */ int sortctree(int *ctree) { int n, startnode=-1; /* find virtual root node (ID=0) */ for(n=0; n>>>\n"); tmpptr = list; *sortlist = list; while (tmpptr != NULL) { (*tmpptr).sortnext = (*tmpptr).succ; (*tmpptr).sortlast = (*tmpptr).pred; tmpptr = (*tmpptr).succ; } while (xchange > 0) { curr = *sortlist; xchange = 0; if (curr == NULL) fprintf(stderr, "Grrrrrrrrr>>>>\n"); while((*curr).sortnext != NULL) { next = (*curr).sortnext; if ((*curr).count >= (*next).count) curr = (*curr).sortnext; else { if ((*curr).sortlast != NULL) (*((*curr).sortlast)).sortnext = next; if (*sortlist == curr) *sortlist = next; (*next).sortlast = (*curr).sortlast; if ((*next).sortnext != NULL) (*((*next).sortnext)).sortlast = curr; (*curr).sortnext = (*next).sortnext; (*curr).sortlast = next; (*next).sortnext = curr; xchange++; } } } } /* sortbynum */ /**********/ /* print puzzling step tree stuctures for checking */ void printfpstrees(treelistitemtype *list) { char ch; treelistitemtype *tmpptr = NULL; tmpptr = list; ch = '-'; while (tmpptr != NULL) { printf ("%c[%2d] %5d %s\n", ch, (*tmpptr).idx, (*tmpptr).count, (*tmpptr).tree); tmpptr = (*tmpptr).succ; ch = ' '; } } /* printfpstrees */ /**********/ /* print sorted puzzling step tree stucture with names */ void fprintffullpstree(FILE *outf, char *treestr) { int count = 0; int idnum = 0; int n; for(n=0; treestr[n] != '\0'; n++){ while(isdigit((int)treestr[n])){ idnum = (10 * idnum) + ((int)treestr[n]-48); n++; count++; } if (count > 0){ # ifdef USEQUOTES fprintf(outf, "'"); # endif (void)fputid(outf, idnum); # ifdef USEQUOTES fprintf(outf, "'"); # endif count = 0; idnum = 0; } fprintf(outf, "%c", treestr[n]); } } /* fprintffullpstree */ /**********/ /* print sorted puzzling step tree stuctures with names */ void fprintfsortedpstrees(FILE *output, treelistitemtype *list, /* tree list */ int itemnum, /* order number */ int itemsum, /* number of trees */ int comment, /* with statistics, or puzzle report ? */ float cutoff) /* cutoff percentage */ { treelistitemtype *tmpptr = NULL; treelistitemtype *slist = NULL; int num = 1; float percent; if (list == NULL) fprintf(stderr, "Grrrrrrrrr>>>>\n"); sortbynum(list, &slist); tmpptr = slist; while (tmpptr != NULL) { percent = (float)(100.0 * (*tmpptr).count / itemsum); if ((cutoff == 0.0) || (cutoff <= percent)) { if (comment) fprintf (output, "[ %d. %d %.2f %d %d %d ]", num++, (*tmpptr).count, percent, (*tmpptr).id, itemnum, itemsum); else { if (num == 1){ fprintf (output, "\n"); fprintf (output, "The following tree(s) occured in more than %.2f%% of the %d puzzling steps.\n", cutoff, itemsum); fprintf (output, "The trees are orderd descending by the number of occurences.\n"); fprintf (output, "\n"); fprintf (output, "\n occurences ID Phylip tree\n"); } fprintf (output, "%2d. %5d %6.2f%% %5d ", num++, (*tmpptr).count, percent, (*tmpptr).id); } fprintffullpstree(output, (*tmpptr).tree); fprintf (output, "\n"); } tmpptr = (*tmpptr).sortnext; } if (!comment) { fprintf (output, "\n"); switch(num) { case 1: fprintf (output, "There were no tree topologies (out of %d) occuring with a percentage \n>= %.2f%% of the %d puzzling steps.\n", itemnum, cutoff, itemsum); break; case 2: fprintf (output, "There was one tree topology (out of %d) occuring with a percentage \n>= %.2f%%.\n", itemnum, cutoff); break; default: fprintf (output, "There were %d tree topologies (out of %d) occuring with a percentage \n>= %.2f%%.\n", num-1, itemnum, cutoff); break; } fprintf (output, "\n"); fprintf (output, "\n"); } } /* fprintfsortedpstrees */ /**********/ /* print sorted tree topologies for checking */ void printfsortedpstrees(treelistitemtype *list) { treelistitemtype *tmpptr = NULL; treelistitemtype *slist = NULL; sortbynum(list, &slist); tmpptr = slist; while (tmpptr != NULL) { printf ("[%2d] %5d %s\n", (*tmpptr).idx, (*tmpptr).count, (*tmpptr).tree); tmpptr = (*tmpptr).sortnext; } } /* printfsortedpstrees */ /*******************************************/ /* end of tree sorting */ /*******************************************/ tree-puzzle-5.2/src/treesort.h0000644000076400001440000001613010073365212012136 /* * treesort.h * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifndef TREESORT_H #define TREESORT_H typedef struct treelistitemtypedummy { struct treelistitemtypedummy *pred; struct treelistitemtypedummy *succ; struct treelistitemtypedummy *sortnext; struct treelistitemtypedummy *sortlast; char *tree; int count; int id; int idx; } treelistitemtype; #include "puzzle.h" #include "util.h" EXTERN treelistitemtype *psteptreelist; EXTERN treelistitemtype *psteptreesortlist; EXTERN int psteptreenum; EXTERN int psteptreesum; /*******************************************/ /* tree sorting */ /*******************************************/ /* compute address of the 4 int (sort key) in the 4 int node */ int ct_sortkeyaddr(int addr); /**********/ /* compute address of the next edge pointer in a 4 int node (0->1->2->0) */ int ct_nextedgeaddr(int addr); /**********/ /* compute address of 1st edge of a 4 int node from node number */ int ct_1stedge(int node); /**********/ /* compute address of 2nd edge of a 4 int node from node number */ int ct_2ndedge(int node); /**********/ /* compute address of 3rd edge of a 4 int node from node number */ int ct_3rdedge(int node); /**********/ /* check whether node 'node' is a leaf (2nd/3rd edge pointer = -1) */ int ct_isleaf(int node, int *ctree); /**********/ /* compute node number of 4 int node from an edge addr. */ int ct_addr2node(int addr); /**********/ /* print graph pointers for checking */ void printctree(int *ctree); /**********/ /* allocate memory for ctree 3 ints pointer plus 1 check byte */ int *initctree(); /**********/ /* free memory of a tree for sorting */ void freectree(int **snodes); /**********/ /* copy subtree recursively */ void copyOTU_trueID(int *ctree, /* in/out: tree array struct */ int *ct_nextnode,/* in/out: next free node */ int ct_curredge,/* in: currend edge to add subtree */ int *ct_nextleaf,/* in/out: next free leaf (0-maxspc) */ int ed, /* in: current edge in puzzling tree */ ONEEDGE *edge, /* in: tree topology */ int *edgeofleaf, /* in: external edge list */ int numleaves, /* in: number of leaves */ int *trueID); /* in: permutation vector */ /**********/ /* copy treestructure to sorting structure */ void copytree_trueID(int *ctree, /* out: copy for effective sorting */ int *trueID, /* in: permutation vector */ ONEEDGE *edgeset, /* in: intermediate tree topology */ int *edgeofleaf, /* dito. */ int numleaves); /* in: number of leaves */ /**********/ /* copy subtree recursively */ void copyOTU(int *ctree, /* in/out: tree array struct */ int *ct_nextnode,/* in/out: next free node */ int ct_curredge,/* in: currend edge to add subtree */ int *ct_nextleaf,/* in/out: next free leaf (0-maxspc) */ int ed, /* in: current edge in puzzling tree */ ONEEDGE *edge, /* in: tree topology */ int *edgeofleaf, /* in: external edge list */ int numleaves); /* in: number of leaves */ /**********/ /* copy treestructure to sorting structure */ void copytree(int *ctree, /* out: copy for effective sorting */ ONEEDGE *edgeset, /* in: intermediate tree topology */ int *edgeofleaf, /* dito. */ int rootleaf, int numleaves); /* in: number of leaves */ /**********/ /* sort subtree from edge recursively by indices */ int sortOTU(int edge, int *ctree); /**********/ /* sort ctree recursively by indices */ int sortctree(int *ctree); /**********/ /* print recursively subtree of edge of sorted tree ctree */ void fprintfsortOTU(FILE *ofp, int edge, int *ctree); /**********/ /* print recursively sorted tree ctree */ int fprintfsortctree(FILE *ofp, int *ctree); /**********/ /* print recursively subtree of edge of sorted tree ctree to string */ void sprintfOTU(char *str, int *len, int edge, int *ctree); /**********/ /* print recursively sorted tree ctree to string */ char *sprintfctree(int *ctree, int strglen); /***********************************************/ /* establish and handle a list of sorted trees */ /***********************************************/ /* initialize structure */ treelistitemtype *inittreelist(int *treenum); /**********/ /* malloc new tree list item */ treelistitemtype *gettreelistitem(); /**********/ /* free whole tree list */ void freetreelist(treelistitemtype **list, int *numitems, int *numsum); /**********/ /* add tree to the tree list */ treelistitemtype *addtree2list(char **tree, /* sorted tree string */ int numtrees, /* how many occurred, e.g. in parallel */ treelistitemtype **list, /* addr. of tree list */ int *numitems, int *numsum); /**********/ /* resort list of trees by number of occurences for output */ void sortbynum(treelistitemtype *list, treelistitemtype **sortlist); /**********/ /* print puzzling step tree stuctures for checking */ void printfpstrees(treelistitemtype *list); /**********/ /* print sorted puzzling step tree stucture with names */ void fprintffullpstree(FILE *outf, char *treestr); /**********/ /* print sorted puzzling step tree stuctures with names */ void fprintfsortedpstrees(FILE *output, treelistitemtype *list, /* tree list */ int itemnum, /* order number */ int itemsum, /* number of trees */ int comment, /* with statistics, or puzzle report ? */ float cutoff); /* cutoff percentage */ /**********/ /* print sorted tree topologies for checking */ void printfsortedpstrees(treelistitemtype *list); /*******************************************/ /* end of tree sorting */ /*******************************************/ #endif /* TREESORT_H */ tree-puzzle-5.2/src/treetest.c0000644000076400001440000005655610073365221012141 /* * treetest.c * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #include #ifndef STDOUT # define STDOUT stdout #endif /*****************************************************************************/ /* ELW/SR Test (Expected Likelihood Weights, Strimmer & Rambaut, 2002) */ /*****************************************************************************/ void elw_test(ivector Alias, dmatrix allsites, int numutrees, int numsites, double siglevel, int numboots, ivector *elw_test_passed, dvector *elw_Support) { /* * Determine posterior probabilties and support values * for each hypothesis and store results in public arrays * posterior, support etc which will automatically be * created by this procedure. * * allsites log-likelihoods of each pattern * Alias map of patterns to sites in sequence * numboots number of bootstraps */ dvector deltaL; /* delta of likelihoods (double[numH]) */ dvector elw_support; /* (double[numH]) */ dvector posterior; /* (double[numH]) */ ivector likelihoodOrder; /* (int[numH]) */ ivector supportOrder; /* (int[numH]) */ dvector rs; /* (int[numH]) */ double sum1; double sum; int numH; /* number of hypotheses */ int numSites; /* number of sites */ int s, p; int i, j, k; /* int j; */ double maxL; double maxLogL; ivector sr_test_res; /* [numutrees]; */ int elw_numboots = 1000; /* number of hypothesis */ numH = numutrees; /* allocate public arrays */ deltaL = new_dvector(numH); elw_support = new_dvector(numH); posterior = new_dvector(numH); likelihoodOrder = new_ivector(numH); supportOrder = new_ivector(numH); sr_test_res = new_ivector(numutrees); *elw_test_passed = sr_test_res; *elw_Support = elw_support; /* number of sites */ numSites = numsites; /******************************************/ /* Compute log-likelihoods, their order, */ /* their deltas and their posteriors */ /******************************************/ /* initialize delta vector for each tree */ for (j = 0; j < numSites; j++) { if (Alias == NULL) { p = j; } else { p = Alias[j]; } for (k = 0; k < numH; k++) { deltaL[k] -= allsites[k][p]; } } /* sort likelihoods -> sorted index list likelihoodOrder */ /* insertion sort */ { int tmp; int idx; for (k=0; k < numH; k++) likelihoodOrder[k] = k; for (j=0; j < numH-1; j++) { idx=j; for (k=j+1; k < numH; k++) { if (deltaL[likelihoodOrder[k]] < deltaL[likelihoodOrder[idx]]) idx=k; } tmp = likelihoodOrder[j]; likelihoodOrder[j] = likelihoodOrder[idx]; likelihoodOrder[idx] = tmp; } } /* Compute deltas */ maxL= -deltaL[likelihoodOrder[0]]; for (j = 0; j < numH; j++) { deltaL[j] = -(deltaL[j]+maxL); } /* compute posterior probabilities */ sum1 = 0.0; for (j = 0; j < numH; j++) { posterior[j] = exp(deltaL[j]); sum1 += posterior[j]; } for (j = 0; j < numH; j++) { posterior[j] = posterior[j]/sum1; } /* reverse sign of delta L */ for (j = 0; j < numH; j++) { deltaL[j] = -deltaL[j]; } deltaL[likelihoodOrder[0]] = 0.0; /* Bootstrap/Resample data */ /***************************/ /* temporary memory */ rs = new_dvector(numH); /* MersenneTwisterFast mt = new MersenneTwisterFast(); */ for (i = 0; i < elw_numboots; i++) { /* num bootstraps */ for (k = 0; k < numH; k++) { rs[k] = 0; } for (j = 0; j < numSites; j++) { /* bootstrapping sites for ...*/ /* int s = mt.nextInt(numSites); */ s = randominteger(numSites); if (Alias == NULL) { p = s; } else { p = Alias[s]; } for (k = 0; k < numH; k++) { /* ...each utree */ /* rs[k] += pLogL[k][p]; */ rs[k] += allsites[k][p]; } } /* find ml hypothesis */ /* maxLogL = findMax(rs); */ { int best = 0; /* can be removed (HAS) */ int idx; double max = rs[0]; for (idx = 1; idx < numH; idx++) { if (rs[idx] > max) { best = idx; /* can be removed (HAS) */ max = rs[idx]; } } maxLogL = max; } /* compute log-likelihood difference */ for (k = 0; k < numH; k++) { rs[k] = rs[k] - maxLogL; } /* compute posteriors and sum over resampled data set */ sum = 0.0; for (k = 0; k < numH; k++) { rs[k] = exp(rs[k]); sum += rs[k]; } for (k = 0; k < numH; k++) { elw_support[k] += rs[k]/sum; } } /* compute support values */ for (j = 0; j < numH; j++) { elw_support[j] = elw_support[j]/elw_numboots; } /* determine order of elw_support (smallest->largest) */ /* HeapSort.sort(elw_support, supportOrder); */ { int tmp; int idx; for (k=0; k < numH; k++) supportOrder[k] = k; for (j=0; j < numH-1; j++) { idx=j; for (k=j+1; k < numH; k++) { if (elw_support[supportOrder[k]] > elw_support[supportOrder[idx]]) idx=k; } tmp = supportOrder[j]; supportOrder[j] = supportOrder[idx]; supportOrder[idx] = tmp; } } sum = 0.0; for (k=0; k maxLogL) { bestH = i; maxLogL = sh_logL[i]; } } /* compute log-likelihood differences to best hypothesis */ for (i = 0; i < numH; i++) { sh_delta[i] = sh_logL[bestH]-sh_logL[i]; } /* allocate temporary memory for resampling procedure */ bs = new_dmatrix(numH,sh_numboots); /* Resample data */ /* MersenneTwisterFast mt = new MersenneTwisterFast(); */ for (i = 0; i < sh_numboots; i++) { for (j = 0; j < numSites; j++) { /* int s = mt.nextInt(numSites); */ s = randominteger(numSites); if (Alias == NULL) { p = s; } else { p = Alias[s]; } for (k = 0; k < numH; k++) { /* rs[k][i] += pLogL[k][p]; */ bs[k][i] += allsites[k][p]; } } } /* center resampled log-likelihoods */ for (i = 0; i < numH; i++) { /* double m = DiscreteStatistics.mean(rs[i]); */ m = 0.0; for (j = 0; j < sh_numboots; j++) { m += bs[i][j]; } m /= sh_numboots; for (j = 0; j < sh_numboots; j++) { bs[i][j] = bs[i][j] - m; } } /* compute resampled log-likelihood differences */ for (i = 0; i < sh_numboots; i++) { /* double max = findMaxInColumn(rs, i); */ { best = 0; colmax = bs[0][i]; for (j = 1; j < numH; j++) { if (bs[j][i] > colmax) { best = j; colmax = bs[j][i]; } } } for (j = 0; j < numH; j++) { bs[j][i] = colmax - bs[j][i]; } } /* compute p-values for each hypothesis */ for (i = 0; i < numH; i++) { count = 0; for (j = 0; j < sh_numboots; j++) { if (bs[i][j] >= sh_delta[i]) { count++; } } sh_pval[i] = (double) count/(double) sh_numboots; if (sh_pval[i] >= sh_prob) { sh_test_res[i] = 1; } else { sh_test_res[i] = 0; } } /* free memory */ free_dmatrix(bs); free_dvector(sh_logL); } /* sh_test */ /* TODO: move to treetest.c */ /* print tree statistics */ void printtreestats(FILE *ofp, dvector ulkl, dvector ulklc, int numutrees, dmatrix allsites, /* tree site log-likelihoods */ dmatrix allsitesc, /* tree site log-likelihoods */ ivector Alias, /* link site -> corresponding site pattern */ int Maxsite, int Numptrn, ivector Weight, int compclock) { int i, j; /* counter variables */ int besttree; /* best tree */ /* for the KH Test (Kishino & Hasegawa, 1989) */ double bestlkl; /* best likelihood */ double difflkl; /* best likelihood difference */ double difflklps; /* best likelihood difference per site */ double temp; double sum; /* variables for the SH Test (Shimodaira & Hasegawa, 1999) */ dvector sh_pval; /* corresponding p-value */ double sh_prob = .05; /* significance level */ int sh_numboots = 1000; /* number of bootstrap samples */ ivector sh_test_res; /* result vector [numutrees]; */ /* variables for the ELW/SR Test (Expected Likelihood Weights) */ /* (Strimmer & Rambaut, 2002) */ dvector elw_support; /* = new double[numH; */ ivector elw_test_res; /* result vector [numutrees]; */ int elw_numboots = 1000; /* number of bootstrap samples */ double elw_prob = .05; /* significance level */ /* variables for the one-sided KH Test using SH */ dvector kh1_pval_tmp; /* temp p-value arry for pairwise SH */ ivector kh1_test_res_tmp; /* temp result arry for pairwise SH */ dvector kh1_pval; /* p-values */ ivector kh1_test_res; /* result vector [numutrees]; */ dvector kh1_allsites_tmp[2]; /* temp arry for pairwise SH test */ int kh1_numboots = 1000; /* number of bootstrap samples */ double kh1_prob = .05; /* significance level */ /* find best tree */ besttree = 0; bestlkl = ulkl[0]; for (i = 1; i < numutrees; i++) { if (ulkl[i] > bestlkl) { besttree = i; bestlkl = ulkl[i]; } } /* one sided KH = pairwise SH test between tree and besttree */ fprintf(STDOUT, "Performing single sided KH test.\n"); fflush(STDOUT); kh1_pval = new_dvector(numutrees); kh1_test_res = new_ivector(numutrees); kh1_allsites_tmp[0] = allsites[besttree]; /* set best tree */ for (i = 0; i < numutrees; i++) { if (i == besttree) { /* if best tree -> no test */ kh1_pval[i] = 1.0; kh1_test_res[i] = 1; } else { /* other wise test pairwise SH */ if ((ulkl[besttree]-ulkl[i]) < MINKHDIFF) { /* if approx equal to best tree -> no test */ kh1_pval[i] = 1.0; kh1_test_res[i] = 1; } else { /* other wise test pairwise SH */ kh1_allsites_tmp[1] = allsites[i]; /* set site log-lh */ sh_test(Alias, kh1_allsites_tmp, 2, Maxsite, kh1_prob, kh1_numboots, &kh1_test_res_tmp, &kh1_pval_tmp); /* pairwise SH */ kh1_pval[i] = kh1_pval_tmp[1]; /* store p-value */ kh1_test_res[i] = kh1_test_res_tmp[1]; /* save result */ } } } free_ivector(kh1_test_res_tmp); /* moved out of loop */ free_dvector(kh1_pval_tmp); /* ELW */ fprintf(STDOUT, "Performing ELW test.\n"); fflush(STDOUT); elw_test(Alias, allsites, numutrees, Maxsite, elw_prob, elw_numboots, &elw_test_res, &elw_support); /* SH */ fprintf(STDOUT, "Performing SH test.\n"); fflush(STDOUT); sh_test(Alias, allsites, numutrees, Maxsite, sh_prob, sh_numboots, &sh_test_res, &sh_pval); /*****************************************************************************/ /* two-sided KH Test (Kishino & Hasegawa, 1989) */ /* and output */ /*****************************************************************************/ fprintf(ofp, "\n\nCOMPARISON OF USER TREES (NO CLOCK)\n\n"); # ifdef KHTWOSIDED fprintf(ofp, "Tree log L difference S.E. Sig. worse p-1sKH p-SH c-ELW \n"); fprintf(ofp, "-------------------------------------------------------------------------------\n"); # else fprintf(ofp, "Tree log L difference S.E. p-1sKH p-SH c-ELW 2sKH\n"); fprintf(ofp, "-------------------------------------------------------------------------------\n"); # endif for (i = 0; i < numutrees; i++) { difflkl = ulkl[besttree]-ulkl[i]; if (difflkl < MINKHDIFF) { /* if lkls (approx) equal to best tree, no difference */ difflkl = 0.0; fprintf(ofp, "%2d %10.2f %8.2f ", i+1, ulkl[i], difflkl); } else { fprintf(ofp, "%2d %10.2f %8.2f ", i+1, ulkl[i], difflkl); } /* fprintf(ofp, "%2d %10.2f %8.2f ", i+1, ulkl[i], difflkl); */ if (i == besttree) { # ifdef KHTWOSIDED fprintf(ofp, " <-------------- best "); # else fprintf(ofp, " <---- best "); /* fprintf(ofp, " <---- best "); */ # endif if (kh1_test_res[i] == 1) fprintf(ofp, " %6.4f +", kh1_pval[i]); else fprintf(ofp, " %6.4f -", kh1_pval[i]); if (sh_test_res[i] == 1) fprintf(ofp, " %6.4f +", sh_pval[i]); else fprintf(ofp, " %6.4f -", sh_pval[i]); if (elw_test_res[i] == 1) fprintf(ofp, " %6.4f +", elw_support[i]); else fprintf(ofp, " %6.4f -", elw_support[i]); # ifdef KHTWOSIDED # else fprintf(ofp, " best"); # endif } else { /* compute variance of Log L differences over sites */ #ifndef USE_WINDOWS difflklps = difflkl/(double)Maxsite; #else difflklps = difflkl/(double)alimaxsite; #endif sum = 0.0; for (j = 0; j < Numptrn; j++) { temp = allsites[besttree][j] - allsites[i][j] - difflklps; sum += temp*temp*Weight[j]; } #ifndef USE_WINDOWS sum = sqrt( fabs(sum/(Maxsite-1.0)*Maxsite) ); #else sum = sqrt(fabs(sum/(alimaxsite-1.0)*alimaxsite)); #endif # ifdef KHTWOSIDED fprintf(ofp, "%11.2f ", sum); if (difflkl > 1.96*sum) fprintf(ofp, "yes "); else fprintf(ofp, "no "); # else fprintf(ofp, "%11.4f ", sum); /* fprintf(ofp, "%11.2f ", sum); */ # endif if (kh1_test_res[i] == 1) fprintf(ofp, " %6.4f +", kh1_pval[i]); else fprintf(ofp, " %6.4f -", kh1_pval[i]); if (sh_test_res[i] == 1) fprintf(ofp, " %6.4f +", sh_pval[i]); else fprintf(ofp, " %6.4f -", sh_pval[i]); if (elw_test_res[i] == 1) fprintf(ofp, " %6.4f +", elw_support[i]); else fprintf(ofp, " %6.4f -", elw_support[i]); # ifdef KHTWOSIDED # else #if 0 if (difflkl > 1.96*sum) fprintf(ofp, " - (diff=%.4f 1.96*sum=%.4e)", difflkl, 1.96*sum); else fprintf(ofp, " + (diff=%.4f 1.96*sum=%.4e)", difflkl, 1.96*sum); #endif if (difflkl > 1.96*sum) fprintf(ofp, " -"); else fprintf(ofp, " +"); # endif } fprintf(ofp, "\n"); } fprintf(ofp, "\nThe columns show the results and p-values of the following tests:\n"); fprintf(ofp, "1sKH - one sided KH test based on pairwise SH tests (Shimodaira-Hasegawa\n"); fprintf(ofp, " 2000, Goldman et al., 2001, Kishino-Hasegawa 1989)\n"); fprintf(ofp, "SH - Shimodaira-Hasegawa test (2000)\n"); fprintf(ofp, "ELW - Expected Likelihood Weight (Strimmer-Rambaut 2002)\n"); fprintf(ofp, "2sKH - two sided Kishino-Hasegawa test (1989)\n"); fprintf(ofp, "\n"); fprintf(ofp, "Plus signs denote the confidence sets. Minus signs denote significant\n"); fprintf(ofp, "exclusion. All tests used 5%% significance level. 1sKH, SH, and ELW\n"); fprintf(ofp, "performed 1000 resamplings using the RELL method.\n"); fprintf(ofp, "1sKH and 2sKH are correct to the 2nd position after the the decimal\n"); fprintf(ofp, "point of the log-likelihoods.\n"); if (compclock) { /* find best tree */ besttree = 0; bestlkl = ulklc[0]; for (i = 1; i < numutrees; i++) if (ulklc[i] > bestlkl) { besttree = i; bestlkl = ulklc[i]; } /* one sided KH */ fprintf(STDOUT, "Performing single sided KH test (clock).\n"); fflush(STDOUT); kh1_pval = new_dvector(numutrees); kh1_test_res = new_ivector(numutrees); kh1_allsites_tmp[0] = allsitesc[besttree]; for (i = 0; i < numutrees; i++) { if (i != besttree) { if ((ulklc[besttree]-ulklc[i]) < MINKHDIFF) { /* if approx equal to best tree -> no test */ kh1_pval[i] = 1.0; kh1_test_res[i] = 1; } else { /* other wise test pairwise SH */ kh1_allsites_tmp[1] = allsitesc[i]; sh_test(Alias, kh1_allsites_tmp, 2, Maxsite, kh1_prob, kh1_numboots, &kh1_test_res_tmp, &kh1_pval_tmp); kh1_pval[i] = kh1_pval_tmp[1]; kh1_test_res[i] = kh1_test_res_tmp[1]; free_ivector(kh1_test_res_tmp); free_dvector(kh1_pval_tmp); } } else { kh1_pval[i] = 1.0; kh1_test_res[i] = 1; } } /* ELW */ fprintf(STDOUT, "Performing ELW test (clock).\n"); fflush(STDOUT); elw_test(Alias, allsitesc, numutrees, Maxsite, elw_prob, elw_numboots, &elw_test_res, &elw_support); /* SH */ fprintf(STDOUT, "Performing SH test (clock).\n"); fflush(STDOUT); sh_test(Alias, allsitesc, numutrees, Maxsite, sh_prob, sh_numboots, &sh_test_res, &sh_pval); fprintf(ofp, "\n\nCOMPARISON OF USER TREES (WITH CLOCK)\n\n"); # ifdef KHTWOSIDED fprintf(ofp, "Tree log L difference S.E. Sig. worse p-1sKH p-SH c-ELW \n"); fprintf(ofp, "-------------------------------------------------------------------------------\n"); # else fprintf(ofp, "Tree log L difference S.E. p-1sKH p-SH c-ELW 2sKH\n"); fprintf(ofp, "-------------------------------------------------------------------------------\n"); # endif for (i = 0; i < numutrees; i++) { difflkl = ulklc[besttree]-ulklc[i]; if (difflkl < MINKHDIFF) { /* if lkls (approx) equal to best tree, no difference */ difflkl = 0.0; fprintf(ofp, "%2d %10.2f %8.2f ", i+1, ulklc[i], difflkl); } else { fprintf(ofp, "%2d %10.2f %8.2f ", i+1, ulklc[i], difflkl); } if (i == besttree) { # ifdef KHTWOSIDED fprintf(ofp, " <-------------- best "); # else fprintf(ofp, " <---- best "); # endif if (kh1_test_res[i] == 1) fprintf(ofp, " %6.4f +", kh1_pval[i]); else fprintf(ofp, " %6.4f -", kh1_pval[i]); if (sh_test_res[i] == 1) fprintf(ofp, " %6.4f +", sh_pval[i]); else fprintf(ofp, " %6.4f -", sh_pval[i]); if (elw_test_res[i] == 1) fprintf(ofp, " %6.4f +", elw_support[i]); else fprintf(ofp, " %6.4f -", elw_support[i]); # ifdef KHTWOSIDED # else fprintf(ofp, " best"); # endif } else { /* compute variance of Log L differences over sites */ #ifndef USE_WINDOWS difflklps = difflkl/(double)Maxsite; #else difflklps = difflkl/(double)alimaxsite; #endif sum = 0.0; for (j = 0; j < Numptrn; j++) { temp = allsitesc[besttree][j] - allsitesc[i][j] - difflklps; sum += temp*temp*Weight[j]; } #ifndef USE_WINDOWS sum = sqrt(fabs(sum/(Maxsite-1.0)*Maxsite)); #else sum = sqrt(fabs(sum/(alimaxsite-1.0)*alimaxsite)); #endif # ifdef KHTWOSIDED fprintf(ofp, "%11.2f ", sum); if (difflkl > 1.96*sum) fprintf(ofp, "yes "); else fprintf(ofp, "no "); # else fprintf(ofp, "%11.2f ", sum); # endif if (kh1_test_res[i] == 1) fprintf(ofp, " %6.4f +", kh1_pval[i]); else fprintf(ofp, " %6.4f -", kh1_pval[i]); if (sh_test_res[i] == 1) fprintf(ofp, " %6.4f +", sh_pval[i]); else fprintf(ofp, " %6.4f -", sh_pval[i]); if (elw_test_res[i] == 1) fprintf(ofp, " %6.4f +", elw_support[i]); else fprintf(ofp, " %6.4f -", elw_support[i]); # ifdef KHTWOSIDED # else if (difflkl > 1.96*sum) fprintf(ofp, " -"); else fprintf(ofp, " +"); # endif } fprintf(ofp, "\n"); } fprintf(ofp, "\nThe columns show the results and p-values of the following tests:\n"); fprintf(ofp, "1sKH - one sided KH test based on pairwise SH tests (Shimodaira-Hasegawa\n"); fprintf(ofp, " 2000, Goldman et al., 2001, Kishino-Hasegawa 1989)\n"); fprintf(ofp, "SH - Shimodaira-Hasegawa test (2000)\n"); fprintf(ofp, "ELW - Expected Likelihood Weight (Strimmer-Rambaut 2002)\n"); fprintf(ofp, "2sKH - two sided Kishino-Hasegawa test (1989)\n"); fprintf(ofp, "\n"); fprintf(ofp, "Plus signs denote the confidence sets. Minus signs denote significant\n"); fprintf(ofp, "exclusion. All tests used 5%% significance level. 1sKH, SH, and ELW\n"); fprintf(ofp, "performed 1000 resamplings using the RELL method.\n"); fprintf(ofp, "1sKH and 2sKH are correct to the 2nd position after the the decimal\n"); fprintf(ofp, "point of the log-likelihoods.\n"); #if 0 fprintf(ofp, "\nColmn 5 gives the results of the (old) two-sided Kishino-Hasegawa test \n"); fprintf(ofp, "following Kishino and Hasegawa (1989). It tests whether a likelihood is \n"); fprintf(ofp, "significantly worse than the best one, marked with 'best'. This test should \n"); fprintf(ofp, "only be used for data not having been determined with the data tested on.\n"); fprintf(ofp, "1sKH is the one-sided KH test (Goldman et al., 2001). It is applicable\n"); fprintf(ofp, "to test whether likelihoods are worse than the lielihood of the ML tree.\n"); fprintf(ofp, "SH tests for the best trees (Shimodaira and Hasegawa, 2000).\n"); fprintf(ofp, "Note that KH, 1sKH, and SH assume to have the 'true' topologies among the tested.\n"); fprintf(ofp, "ELW (Expected likelihood weights) seems to work even without this restriction\n"); fprintf(ofp, "(Strimmer and Rambaut, 2002). Still plausible trees should be among the tested.\n"); fprintf(ofp, "For 1sKH, SH, and ELW plus signs '+' mark the topologies belonging to the\n"); fprintf(ofp, "confidence sets the numbers give the p-values (1sKH and SH) or the confidence\n"); fprintf(ofp, "weight (ELW).\n"); fprintf(ofp, "All tests used 5%% significance level. 1sKH, SH, and ELW used 1000 resamplings.\n"); #endif } } /* printtreestats */ /********************************************************/ tree-puzzle-5.2/src/treetest.h0000644000076400001440000000433310073365226012135 /* * treetest.h * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifndef TREETEST_H #define TREETEST_H #include /* minimum log-lh difference to best log-lh to be different */ #define MINKHDIFF 0.005 /*****************************************************************************/ /* ELW/SR Test (Expected Likelihood Weights, Strimmer & Rambaut, 2002) */ /*****************************************************************************/ void elw_test(ivector Alias, dmatrix allsites, int numutrees, int numsites, double siglevel, int numboots, ivector *elw_test_passed, dvector *elw_Support); /*****************************************************************************/ /* SH Test (Shimodaira & Hasegawa, 1999) */ /*****************************************************************************/ void sh_test(ivector Alias, /* site pattern translat array */ dmatrix allsites, /* tree site log-likelihoods */ int numutrees, /* number of trees */ int numsites, /* number of sites */ double siglevel, /* significance level to test */ int numboots, /* number of bootstraps to draw */ ivector *sh_test_passed, /* has tree passed tests */ dvector *sh_Pval); /* and p-value */ /* print tree statistics */ void printtreestats(FILE *ofp, dvector ulkl, dvector ulklc, int numutrees, dmatrix allsites, /* tree site log-likelihoods */ dmatrix allsitesc, /* tree site log-likelihoods */ ivector Alias, /* link site -> corresponding site pattern */ int Maxsite, int Numptrn, ivector Weight, int compclock); #endif /* TREETEST_H */ tree-puzzle-5.2/src/README0000644000076400001440000000004307152034631010774 Sources of the TREE-PUZZLE package tree-puzzle-5.2/src/pstep-deglob.c0000644000076400001440000004075210073365233012661 /* * pstep-deglob.c (obsolete) * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #define EXTERN extern #include #include #include"puzzle.h" /* #include"util.h" */ /* #include"pstep.h" */ #include /******************************************************************************/ /* functions for representing and building puzzling step trees */ /******************************************************************************/ /* initialize tree with the following starting configuration * A(=0) * [up =NULL] * [downleft =1] * [downright=2] * * o * | * | * +-------------+--------------+ * | | * | | * o o * * C(=1) B(=2) * [up =0] [up =0] * [downleft =NULL] [downleft =NULL] * [downright=NULL] [downright=NULL] * * nextedge = 3 * nextleaf = 3 * and set according edge maps * */ void inittree_orig(ONEEDGE_ORIG **edge, /* out: new array of edges */ int **edgeofleaf,/* out: array of external edge ptrs */ int Maxspc, /* in: Number of species (n) */ int Maxbrnch, /* in: Number of branches (2n-3) */ int *nextedge, /* out: next free edge index (=3) */ int *nextleaf) /* out: next free leaf index (=3) */ { int i; ONEEDGE_ORIG *tmpedge; int *tmpedgeofleaf; /* allocate the memory for the whole tree */ /* allocate memory for vector with all the edges of the tree */ tmpedge = (ONEEDGE_ORIG *) calloc((size_t) Maxbrnch, sizeof(ONEEDGE_ORIG) ); if (tmpedge == NULL) maerror("edge in inittree"); *edge = tmpedge; /* allocate memory for vetmpctor with edge numbers of leaves */ tmpedgeofleaf = (int *) calloc((size_t) Maxspc, sizeof(int) ); if (tmpedgeofleaf == NULL) maerror("edgeofleaf in inittree"); *edgeofleaf = tmpedgeofleaf; /* allocate memory for all the edges the edge map */ for (i = 0; i < Maxbrnch; i++) { (tmpedge)[i].edgemap = (int *) calloc((size_t) Maxbrnch, sizeof(int) ); if (tmpedge[i].edgemap == NULL) maerror("edgemap in inittree"); } /* number all edges */ for (i = 0; i < Maxbrnch; i++) tmpedge[i].numedge = i; /* initialize tree */ *nextedge = 3; *nextleaf = 3; /* edge maps */ (tmpedge[0].edgemap)[0] = 0; /* you are on the right edge */ (tmpedge[0].edgemap)[1] = 4; /* go down left for leaf 1 */ (tmpedge[0].edgemap)[2] = 5; /* go down right for leaf 2 */ (tmpedge[1].edgemap)[0] = 1; /* go up for leaf 0 */ (tmpedge[1].edgemap)[1] = 0; /* you are on the right edge */ (tmpedge[1].edgemap)[2] = 3; /* go up/down right for leaf 2 */ (tmpedge[2].edgemap)[0] = 1; /* go up for leaf 0 */ (tmpedge[2].edgemap)[1] = 2; /* go up/down left for leaf 1 */ (tmpedge[2].edgemap)[2] = 0; /* you are on the right edge */ /* interconnection */ tmpedge[0].up = NULL; tmpedge[0].downleft = &tmpedge[1]; tmpedge[0].downright = &tmpedge[2]; tmpedge[1].up = &tmpedge[0]; tmpedge[1].downleft = NULL; tmpedge[1].downright = NULL; tmpedge[2].up = &tmpedge[0]; tmpedge[2].downleft = NULL; tmpedge[2].downright = NULL; /* edges of leaves */ tmpedgeofleaf[0] = 0; tmpedgeofleaf[1] = 1; tmpedgeofleaf[2] = 2; } /* inittree */ /* add next leaf on the specified edge */ void addnextleaf_orig(int dockedge, /* insert here */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc, /* No. of species */ int Maxbrnch, /* No. of branches */ int *in_nextedge, /* next free edge idx */ int *in_nextleaf) /* next free leaf idx */ { int i; int nextedge; int nextleaf; nextedge=*in_nextedge; nextleaf=*in_nextleaf; if (dockedge >= nextedge) { /* Trying to add leaf nextleaf to nonexisting edge dockedge */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR F TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } if (nextleaf >= Maxspc) { /* Trying to add leaf nextleaf to a tree with Maxspc leaves */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR G TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } /* necessary change in edgeofleaf if dockedge == edgeofleaf[0] */ if (edgeofleaf[0] == dockedge) edgeofleaf[0] = nextedge; /* adding nextedge to the tree */ edge[nextedge].up = edge[dockedge].up; edge[nextedge].downleft = &edge[dockedge]; edge[nextedge].downright = &edge[nextedge+1]; edge[dockedge].up = &edge[nextedge]; if (edge[nextedge].up != NULL) { if ( ((edge[nextedge].up)->downleft) == &edge[dockedge] ) (edge[nextedge].up)->downleft = &edge[nextedge]; else (edge[nextedge].up)->downright = &edge[nextedge]; } /* adding nextedge + 1 to the tree */ edge[nextedge+1].up = &edge[nextedge]; edge[nextedge+1].downleft = NULL; edge[nextedge+1].downright = NULL; edgeofleaf[nextleaf] = nextedge+1; /* the two new edges get info about the old edges */ /* nextedge */ for (i = 0; i < nextedge; i++) { switch ( (edge[dockedge].edgemap)[i] ) { /* down right changes to down left */ case 5: (edge[nextedge].edgemap)[i] = 4; break; /* null changes to down left */ case 0: (edge[nextedge].edgemap)[i] = 4; break; default: (edge[nextedge].edgemap)[i] = (edge[dockedge].edgemap)[i]; break; } } /* nextedge + 1 */ for (i = 0; i < nextedge; i++) { switch ( (edge[dockedge].edgemap)[i] ) { /* up/down left changes to up */ case 2: (edge[nextedge+1].edgemap)[i] = 1; break; /* up/down right changes to up */ case 3: (edge[nextedge+1].edgemap)[i] = 1; break; /* down left changes to up/down left */ case 4: (edge[nextedge+1].edgemap)[i] = 2; break; /* down right changes to up/down left */ case 5: (edge[nextedge+1].edgemap)[i] = 2; break; /* null changes to up/down left */ case 0: (edge[nextedge+1].edgemap)[i] = 2; break; /* up stays up */ default: (edge[nextedge+1].edgemap)[i] = (edge[dockedge].edgemap)[i]; break; } } /* dockedge */ for (i = 0; i < nextedge; i++) { switch ( (edge[dockedge].edgemap)[i] ) { /* up/down right changes to up */ case 3: (edge[dockedge].edgemap)[i] = 1; break; /* up/down left changes to up */ case 2: (edge[dockedge].edgemap)[i] = 1; break; default: break; } } /* all edgemaps are updated for the two new edges */ /* nextedge */ (edge[nextedge].edgemap)[nextedge] = 0; (edge[nextedge].edgemap)[nextedge+1] = 5; /* down right */ /* nextedge + 1 */ (edge[nextedge+1].edgemap)[nextedge] = 1; /* up */ (edge[nextedge+1].edgemap)[nextedge+1] = 0; /* all other edges */ for (i = 0; i < nextedge; i++) { (edge[i].edgemap)[nextedge] = (edge[i].edgemap)[dockedge]; (edge[i].edgemap)[nextedge+1] = (edge[i].edgemap)[dockedge]; } /* an extra for dockedge */ (edge[dockedge].edgemap)[nextedge] = 1; /* up */ (edge[dockedge].edgemap)[nextedge+1] = 3; /* up/down right */ nextleaf++; nextedge = nextedge + 2; *in_nextedge=nextedge; *in_nextleaf=nextleaf; } /* addnextleaf */ /* free memory (to be called after inittree) */ void freetree_orig(ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc) /* No. of species */ { int i; for (i = 0; i < 2 * Maxspc - 3; i++) free(edge[i].edgemap); free(edge); free(edgeofleaf); } /* freetree */ /* trueID (HAS) */ /* writes OTU sitting on edge ed */ void writeOTU_orig(FILE *outfp, /* output file */ int ed, /* edge to subtree */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *column, /* current screen depth */ int *trueID) /* species permutation */ { int i; /* test whether we are on a leaf */ if (edge[ed].downright == NULL && edge[ed].downleft == NULL) { for (i = 1; i < nextleaf; i++) { if (edgeofleaf[i] == ed) { /* i is the leaf of ed */ /* trueID (HAS) */ *column += fputid(outfp, trueID[i]); return; } } } /* we are NOT on a leaf */ fprintf(outfp, "("); (*column)++; /* trueID (HAS) */ writeOTU_orig(outfp, edge[ed].downleft->numedge, edge, edgeofleaf, nextedge, nextleaf, column, trueID); fprintf(outfp, ","); (*column)++; (*column)++; if (*column > 55) { *column = 2; fprintf(outfp, "\n "); } /* trueID (HAS) */ writeOTU_orig(outfp, edge[ed].downright->numedge, edge, edgeofleaf, nextedge, nextleaf, column, trueID); fprintf(outfp, ")"); (*column)++; } /* writeOTU */ /* trueID (HAS) */ /* write tree */ void writetree_orig(FILE *outfp, /* output file */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *trueID) /* species permutation */ { column_orig = 1; fprintf(outfp, "("); column_orig += fputid(outfp, trueID[0]) + 3; fprintf(outfp, ","); writeOTU_orig(outfp, edge[edgeofleaf[0]].downleft->numedge, edge, edgeofleaf, nextedge, nextleaf, &column_orig, trueID); column_orig++; column_orig++; fprintf(outfp, ","); writeOTU_orig(outfp, edge[edgeofleaf[0]].downright->numedge, edge, edgeofleaf, nextedge, nextleaf, &column_orig, trueID); fprintf(outfp, ");\n"); } /* writetree */ /* clear all edgeinfos */ void resetedgeinfo_orig(ONEEDGE_ORIG *edge, /* edge array */ int nextedge) /* next free edge idx */ { int i; for (i = 0; i < nextedge; i++) edge[i].edgeinfo = 0; } /* resetedgeinfo */ /* increment all edgeinfo between leaf A and B */ void incrementedgeinfo_orig(int A, /* start leaf of penalty path */ int B, /* start leaf of penalty path */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf) /* ext. edge idx array */ { int curredge, finaledge, nextstep; if (A == B) return; finaledge = edgeofleaf[B]; curredge = edgeofleaf[A]; edge[curredge].edgeinfo = edge[curredge].edgeinfo + 1; while (curredge != finaledge) { nextstep = (edge[curredge].edgemap)[finaledge]; switch (nextstep) { /* up */ case 1: curredge = (edge[curredge].up)->numedge; break; /* up/down left */ case 2: curredge = ((edge[curredge].up)->downleft)->numedge; break; /* up/down right */ case 3: curredge = ((edge[curredge].up)->downright)->numedge; break; /* down left */ case 4: curredge = (edge[curredge].downleft)->numedge; break; /* down right */ case 5: curredge = (edge[curredge].downright)->numedge; break; } edge[curredge].edgeinfo = edge[curredge].edgeinfo + 1; } } /* incrementedgeinfo */ /* checks which edge has the lowest edgeinfo if there are several edges with the same lowest edgeinfo, one of them will be selected randomly */ void minimumedgeinfo_orig(ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *out_minedge, /* minimum edge set */ uli *out_mininfo) /* minumum penalty */ { int i, k, howmany, randomnum; int minedge; /* minimum edge set */ uli mininfo; /* minumum penalty */ howmany = 1; minedge = 0; mininfo = edge[0].edgeinfo; for (i = 1; i < nextedge; i++) if (edge[i].edgeinfo <= mininfo) { if (edge[i].edgeinfo == mininfo) { howmany++; } else { minedge = i; mininfo = edge[i].edgeinfo; howmany = 1; } } if (howmany > 1) { /* draw random edge */ randomnum = randominteger(howmany) + 1; /* 1 to howmany */ i = -1; for (k = 0; k < randomnum; k++) { do { i++; } while (edge[i].edgeinfo != mininfo); minedge = i; } } *out_minedge=minedge; *out_mininfo=mininfo; } /* minimumedgeinfo */ tree-puzzle-5.2/src/pstep-deglob.h0000644000076400001440000001424610073365241012664 /* * pstep-deglob.h (obsolete) * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifndef PSTEP_ORIG_H #define PSTEP_ORIG_H #include #include #include"puzzle.h" #include"util.h" /* #include"newpstep.h" */ #include #ifndef ONEEDGE_DEFINED #define ONEEDGE_DEFINED /* tree structure */ typedef struct oneedge { /* pointer to other three edges */ struct oneedge *up; struct oneedge *downleft; struct oneedge *downright; int numedge; /* number of edge (index) */ uli edgeinfo; /* value of this edge (penalty) */ int *edgemap; /* pointer to the local edgemap array */ } ONEEDGE_ORIG; #endif /* ! ONEEDGE_DEFINED */ EXTERN int *edgeofleaf_orig; /* vector with edge number of all leaves */ EXTERN int minedge_orig; /* edge with minimum edgeinfo */ EXTERN int nextedge_orig; /* number of edges in the current tree */ EXTERN int nextleaf_orig; /* next leaf to add to tree */ EXTERN ONEEDGE_ORIG *edge_orig; /* vector with all the edges of the tree */ uli *splitcomp_orig; /* bipartition storage */ uli *splitfreqs_orig; /* frequencies of all different splits of all trees */ uli *splitpatterns_orig; /* all different splits of all trees */ #if 0 EXTERN int Maxbrnch; /* 2*Maxspc - 3 */ EXTERN int Maxspc; /* Maxspc */ #endif ivector trueID_orig; int column_orig; uli mininfo_orig; /* value of edgeinfo on minedge */ /*****************************************************************************/ /* functions for representing and building puzzling step trees */ /*****************************************************************************/ /* initialize tree with the following starting configuration * * 2 * 0 +------- C(=2) * A(=0) -----+ * +------- B(=1) * 1 * * * A(=0) * [up =NULL] * [downleft =1] * [downright=2] * * o * | * | * +-------------+--------------+ * | | * | | * o o * * C(=1) B(=2) * [up =0] [up =0] * [downleft =NULL] [downleft =NULL] * [downright=NULL] [downright=NULL] * * nextedge = 3 * nextleaf = 3 * and set according edge maps * */ void inittree_orig(ONEEDGE_ORIG **edge, /* out: new array of edges */ int **edgeofleaf,/* out: array of external edge ptrs */ int Maxspc, /* in: Number of species (n) */ int Maxbrnch, /* in: Number of branches (2n-3) */ int *nextedge, /* out: next free edge index (=3) */ int *nextleaf); /* out: next free leaf index (=3) */ /* add next leaf on the specified edge */ void addnextleaf_orig(int dockedge, /* insert here */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc, /* No. of species */ int Maxbrnch, /* No. of branches */ int *nextedge, /* next free edge idx */ int *nextleaf); /* next free leaf idx */ /* free memory (to be called after inittree) */ void freetree_orig(ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc); /* No. of species */ /* writes OTU sitting on edge ed */ void writeOTU_orig(FILE *outfp, /* output file */ int ed, /* edge to subtree */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *column, /* current screen depth */ int *trueID); /* species permutation */ /* write tree */ void writetree_orig(FILE *outfp, /* output file */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *trueID); /* species permutation */ /* clear all edgeinfos */ void resetedgeinfo_orig(ONEEDGE_ORIG *edge, /* edge array */ int nextedge); /* next free edge idx */ /* increment all edgeinfo between leaf A and B */ void incrementedgeinfo_orig(int A, /* start leaf of penalty path */ int B, /* start leaf of penalty path */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf); /* ext. edge idx array */ /* checks which edge has the lowest edgeinfo if there are several edges with the same lowest edgeinfo, one of them will be selected randomly */ void minimumedgeinfo_orig(ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *minedge, /* minimum edge set */ uli *mininfo); /* minumum penalty */ #endif /* PSTEP_ORIG_H */ tree-puzzle-5.2/src/sched.c0000644000076400001440000002474710073365246011374 /* * sched.c * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifdef HAVE_CONFIG_H # include #endif #include #include #include #include "sched.h" /* #include "ppuzzle.h" */ #define STDOUT stdout #ifndef PARALLEL /* because printf() runs significantly faster */ /* than fprintf(stdout) on an Apple McIntosh */ /* (HS) */ # define FPRINTF printf # define STDOUTFILE #else # define FPRINTF fprintf # define STDOUTFILE STDOUT, #endif int scinit; int ssinit; int fscinit; int gssinit; int tssinit; int n, chunksize; int p; #ifdef SCHEDTEST schedtype testsched; #endif void printsched(schedtype sch) { fprintf(STDOUT, "Current scheduling status:\n"); fprintf(STDOUT, " truetasks=%5ld - alltasks=%5ld - numtasks=%5ld - numprocs=%5d\n", sch.truetasks, sch.alltasks, sch.numtasks, sch.numprocs); fprintf(STDOUT, " delta =%5lu - overhead=%5lu - rest =%5lu - inited =%5d\n", sch.delta, sch.overhead, sch.rest, sch.inited); fprintf(STDOUT, " nconst =%5d - fconst =%5f - lconst =%5f - kconst =%5f\n", sch.nconst, sch.fconst, sch.lconst, sch.kconst); } /* printsched */ void initsched(schedtype *sch, uli tasks, int procs, uli minchunk) { if (minchunk < 1) minchunk = 1; (*sch).minchunk = minchunk; (*sch).truetasks = tasks; (*sch).rest = (int)((*sch).truetasks % (*sch).minchunk); (*sch).alltasks = (tasks - (*sch).rest); (*sch).numtasks = (*sch).alltasks; (*sch).numprocs = procs; (*sch).delta = 0; (*sch).overhead = 0; (*sch).nconst = 0; (*sch).fconst = 0; (*sch).lconst = 0; (*sch).kconst = 0; (*sch).inited = 0; # ifdef PVERBOSE1 printsched(*sch); # endif /* PVERBOSE1 */ } /* initsched */ /************************************** * Static Chunking **************************************/ uli sc(schedtype *sch) { uli tmp; if ((*sch).inited == 0) { (*sch).overhead = (*sch).alltasks % (*sch).numprocs; (*sch).delta = ((*sch).alltasks - (*sch).overhead) / (*sch).numprocs; (*sch).inited ++; } if (!(*sch).overhead) { if ((*sch).numtasks >= (*sch).delta) tmp = (uli)(*sch).delta; else tmp = 0; } else { if ((*sch).numtasks >= ((*sch).delta + 1)) { tmp = (uli)(*sch).delta + 1; (*sch).overhead--; } else tmp = 0; } /* correction */ if ((tmp % (*sch).minchunk) > 0) { tmp += (*sch).minchunk - (tmp % (*sch).minchunk); } (*sch).numtasks -= tmp; if ((*sch).numtasks == 0) { tmp += (uli)(*sch).rest; (*sch).rest = 0; } return tmp; } /* SC */ /************************************** * Self Scheduling **************************************/ uli ss(schedtype *sch) { uli tmp; if ((*sch).inited == 0) { (*sch).inited ++; } if ((*sch).numtasks >= 1) tmp = 1; else tmp = (*sch).numtasks; /* correction */ if ((tmp % (*sch).minchunk) > 0) { tmp += (*sch).minchunk - (tmp % (*sch).minchunk); } (*sch).numtasks -= tmp; if ((*sch).numtasks == 0) { tmp += (uli)(*sch).rest; (*sch).rest = 0; } return tmp; } /* SS */ /************************************** * fixed-size chunking **************************************/ int fsc() { static int R ; static int delta ; static int overhead; int tmp; if (fscinit == 0) { R = n; overhead = n % p; delta = (n - overhead) / p; fscinit ++; } if (!overhead) { if (R >= delta) tmp = delta; else tmp = 0; } else { if (R >= (delta + 1)) { tmp = delta + 1; overhead--; } else tmp = 0; } R -= tmp; return tmp; } /* FSC */ /************************************** * Guided Self Scheduling **************************************/ uli gss(schedtype *sch) { uli tmp; if ((*sch).inited == 0) { (*sch).inited ++; } if ((*sch).numtasks >= 1) { tmp = (uli)ceil((*sch).numtasks / (*sch).numprocs); if (tmp == 0) tmp = 1; } else tmp = 0; /* correction */ if ((tmp % (*sch).minchunk) > 0) { tmp += (*sch).minchunk - (tmp % (*sch).minchunk); } (*sch).numtasks -= tmp; if ((*sch).numtasks == 0) { tmp += (uli)(*sch).rest; (*sch).rest = 0; } return tmp; } /* GSS */ /************************************** * Smooth Guided Self Scheduling **************************************/ uli sgss(schedtype *sch) { uli tmp; if ((*sch).inited == 0) { (*sch).inited ++; } if ((*sch).numtasks >= 1) { tmp = (uli)ceil(((*sch).numtasks / (*sch).numprocs) / 2); if (tmp == 0) tmp = 1; } else tmp = 0; /* correction */ if ((tmp % (*sch).minchunk) > 0) { tmp += (*sch).minchunk - (tmp % (*sch).minchunk); } (*sch).numtasks -= tmp; if ((*sch).numtasks == 0) { tmp += (uli)(*sch).rest; (*sch).rest = 0; } return tmp; } /* SGSS */ /************************************** * Trapezoid Self Scheduling **************************************/ uli tss(schedtype *sch) { uli tmp; if ((*sch).inited == 0) { (*sch).fconst = ceil((*sch).numtasks / (2*(*sch).numprocs)); if ((*sch).fconst == 0) (*sch).fconst = 1; (*sch).lconst = 1; (*sch).nconst = ceil( (2*n) / ((*sch).fconst + (*sch).lconst) ); (*sch).ddelta = (((*sch).fconst - (*sch).lconst) / ((*sch).nconst - 1)); (*sch).kconst = (*sch).fconst; fprintf(STDOUT, "f = n/2p = %.2f ; l = %.2f\n", (*sch).fconst, (*sch).lconst); fprintf(STDOUT, "N = 2n/(f+l) = %d ; delta = (f-l)/(N-1) = %.2f\n", (*sch).nconst, (*sch).ddelta); (*sch).inited ++; } if ((*sch).kconst <= (double) (*sch).numtasks) { tmp = (uli)ceil((*sch).kconst); (*sch).kconst -= (*sch).ddelta; } else { tmp = (uli)(*sch).numtasks; (*sch).kconst = 0.0; } /* correction */ if ((tmp % (*sch).minchunk) > 0) { tmp += (*sch).minchunk - (tmp % (*sch).minchunk); } (*sch).numtasks -= tmp; if ((*sch).numtasks == 0) { tmp += (uli)(*sch).rest; (*sch).rest = 0; } return tmp; } /* TSS */ /******************/ #ifdef SCHEDTEST uli numquarts(int maxspc) { uli tmp; int a, b, c, d; if (maxspc < 4) return (uli)0; else { maxspc--; a = maxspc-3; b = maxspc-2; c = maxspc-1; d = maxspc; tmp = (uli) 1 + a + (uli) b * (b-1) / 2 + (uli) c * (c-1) * (c-2) / 6 + (uli) d * (d-1) * (d-2) * (d-3) / 24; return (tmp); } } /* numquarts */ #endif /************************************** * main **************************************/ #ifdef SCHEDTEST int main(int argc, char *argv[]) { int tcount, count, lastsize, size; if ((argc > 4) || (argc < 3)) { fprintf(STDOUT, "\n\n Usage: %s <# species> <# processors> []\n\n", argv[0]); exit(1); } chunksize = 1; switch(argc) { case 4: chunksize = atoi(argv[3]); case 3: n = numquarts(atoi(argv[1])); p = atoi(argv[2]); } fprintf(STDOUT, "proc=%6d\n", p); fprintf(STDOUT, "task=%6d\n", n); initsched(&testsched, n, p, chunksize); printsched(testsched); count=1; tcount = 0; fprintf(STDOUT, "\n\n---------------------------\n"); fprintf(STDOUT, "SC(sched) - Static Chunking\n"); fprintf(STDOUT, "---------------------------\n\n"); do { size = sc(&testsched); if (size > 0) {fprintf(STDOUT, "%6d. chunk = %6d %c\n", count++, size , (size%chunksize) ? '!' : ' '); tcount+=size;} else fprintf(STDOUT, "%d tasks in %d chunks\n", tcount, (count-1)); } while (size > 0); initsched(&testsched, n, p, chunksize); printsched(testsched); count=1; tcount = 0; fprintf(STDOUT, "\n\n---------------------------\n"); fprintf(STDOUT, "SS(sched) - Self Scheduling\n"); fprintf(STDOUT, "---------------------------\n\n"); do { size = ss(&testsched); if (size > 0) {if (count==1) fprintf(STDOUT, "%6d. chunk = %6d %c\n", count++, size , (size%chunksize) ? '!' : ' '); count++; tcount+=size; lastsize = size;} else {fprintf(STDOUT, " ...\n"); fprintf(STDOUT, "%6d. chunk = %6d %c\n", count++, lastsize , (lastsize%chunksize) ? '!' : ' '); fprintf(STDOUT, "%d tasks in %d chunks\n", tcount, (count-1));} } while (size > 0); /**/ count=1; tcount = 0; fprintf(STDOUT, "\n\n---------------------------\n"); fprintf(STDOUT, "FSC() - Fixed-Size Chunking\n"); fprintf(STDOUT, "---------------------------\n\n"); do { size = fsc(); if (size > 0) {fprintf(STDOUT, "%6d. chunk = %6d %c\n", count++, size , (size%chunksize) ? '!' : ' '); tcount+=size;} else fprintf(STDOUT, "%d tasks in %d chunks\n", tcount, (count-1)); } while (size > 0); /**/ initsched(&testsched, n, p, chunksize); printsched(testsched); count=1; tcount = 0; fprintf(STDOUT, "\n\n-----------------------------------\n"); fprintf(STDOUT, "GSS(sched) - Guided Self Scheduling\n"); fprintf(STDOUT, "-----------------------------------\n\n"); do { size = gss(&testsched); if (size > 0) {fprintf(STDOUT, "%6d. chunk = %6d %c\n", count++, size , (size%chunksize) ? '!' : ' '); tcount+=size;} else fprintf(STDOUT, "%d tasks in %d chunks\n", tcount, (count-1)); } while (size > 0); initsched(&testsched, n, p, chunksize); printsched(testsched); count=1; tcount = 0; fprintf(STDOUT, "\n\n--------------------------------------\n"); fprintf(STDOUT, "TSS(sched) - Trapezoid Self Scheduling\n"); fprintf(STDOUT, "--------------------------------------\n\n"); do { size = tss(&testsched); if (size > 0) {fprintf(STDOUT, "%6d. chunk = %6d %c\n", count++, size , (size%chunksize) ? '!' : ' '); tcount+=size;} else fprintf(STDOUT, "%d tasks in %d chunks\n", tcount, (count-1)); } while (size > 0); return (0); } /* main */ #endif tree-puzzle-5.2/src/sched.h0000644000076400001440000000440110073365253011360 /* * sched.h * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifndef SCHED_H #define SCHED_H #ifndef SCHEDTEST # include "util.h" #else typedef unsigned long int uli; #endif typedef struct sched_t{ uli truetasks; /* number of tasks to be scheduled, as given by user */ int numprocs; /* number of processors (p=PP_numprocs-1, master-worker scheme */ uli minchunk; /* pre-packing: task-size must be dividable by */ uli rest; /* part of tasks not fitting into batches with minchunk-dividable size */ /* truetasks mod minchunk */ uli alltasks; /* number of tasks to be scheduled in minchunk-size batches */ /* truetasks - rest */ uli numtasks; /* tasks not yet scheduled (init: numtasks = alltasks) */ uli overhead; /* SC,FSC: remainder from dividing alltasks into numprocs batches */ /* alltasks mod numprocs */ uli delta; /* SC,FSC: initial batch size */ /* (alltasks - overhead) / numprocs = alltasks % numprocs */ double fconst; /* TSS: start (first) batch size (f) */ double lconst; /* TSS: last batch size (l) */ double kconst; /* TSS: actual batch size (k) */ double ddelta; /* TSS: amount of decrease */ int nconst; /* TSS: needed to compute ddelta (N) */ int inited; /* initialized flag for parameter initialization by scheduler */ } schedtype; void num2quart(uli qnum, int *a, int *b, int *c, int *d); uli numquarts(int maxspc); uli quart2num (int a, int b, int c, int d); void printsched(schedtype sch); void initsched(schedtype *sch, uli tasks, int procs, uli minchunk); uli sc(schedtype *sch); uli gss(schedtype *sch); uli sgss(schedtype *sch); uli tss(schedtype *sch); #endif /* SCHED_H */ tree-puzzle-5.2/src/pstep-split.c0000644000076400001440000006571610073365261012570 /* * pstep-split.c * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ /* split based O(n^4) algorithm */ #ifdef HAVE_CONFIG_H # include #endif #define EXTERN extern #include #include #include"puzzle.h" /* #include"util.h" */ #include"pstep-split.h" #if PARALLEL # include "ppuzzle.h" #endif /******************************************************************************/ /* functions for representing and building puzzling step trees */ /******************************************************************************/ /* initialize tree with the following starting configuration * * 2 * 0 +------- C(=2) * A(=0) -----+ * +------- B(=1) * 1 * * * A(=0) * [up =NULL] * [downleft =1] * [downright=2] * [cluster(up)=0] * [cluster(down)=1,2] * [upsize=1] * [downsize=2] * * o * | * | * +-------------+--------------+ * | | * | | * o o * * C(=1) B(=2) * [up =0] [up =0] * [downleft =NULL] [downleft =NULL] * [downright=NULL] [downright=NULL] * [cluster(up)=0,2] [cluster(up)=0] * [cluster(down)=1] [cluster(down)=2] * [upsize=2] [upsize=2] * [downsize=1] [downsize=1] * * nextedge = 3 * nextleaf = 3 * and set according edge maps * */ void inittree_split(ONEEDGE_SPLIT **edge, /* out: new array of edges */ int **edgeofleaf,/* out: array of external edge ptrs */ int Maxspc, /* in: Number of species (n) */ int Maxbrnch, /* in: Number of branches (2n-3) */ int *nextedge, /* out: next free edge index (=3) */ int *nextleaf) /* out: next free leaf index (=3) */ { int i; ONEEDGE_SPLIT *tmpedge; int *tmpedgeofleaf; /* allocate the memory for the whole tree */ /* allocate memory for vector with all the edges of the tree */ tmpedge = (ONEEDGE_SPLIT *) calloc((size_t) Maxbrnch, sizeof(ONEEDGE_SPLIT) ); if (tmpedge == NULL) maerror("edge in inittree"); *edge = tmpedge; /* allocate memory for vetmpctor with edge numbers of leaves */ tmpedgeofleaf = (int *) calloc((size_t) Maxspc, sizeof(int) ); if (tmpedgeofleaf == NULL) maerror("edgeofleaf in inittree"); *edgeofleaf = tmpedgeofleaf; /* allocate memory for all the edges the split map */ for (i = 0; i < Maxbrnch; i++) { (tmpedge)[i].split = (int *) calloc((size_t) Maxspc, sizeof(int) ); if (tmpedge[i].split == NULL) maerror("split array in inittree"); #if 0 (tmpedge)[i].downcluster = (int *) calloc((size_t) Maxspc, sizeof(int) ); if (tmpedge[i].downcluster == NULL) maerror("downcluster edgemap in inittree"); /* old _orig algorithm */ (tmpedge)[i].edgemap = (int *) calloc((size_t) Maxbrnch, sizeof(int) ); if (tmpedge[i].edgemap == NULL) maerror("edgemap in inittree"); #endif } /* number all edges */ for (i = 0; i < Maxbrnch; i++) tmpedge[i].numedge = i; /* initialize tree */ *nextedge = 3; *nextleaf = 3; #if 0 /* edge maps */ (tmpedge[0].edgemap)[0] = 0; /* you are on the right edge */ (tmpedge[0].edgemap)[1] = 4; /* go down left for leaf 1 */ (tmpedge[0].edgemap)[2] = 5; /* go down right for leaf 2 */ (tmpedge[1].edgemap)[0] = 1; /* go up for leaf 0 */ (tmpedge[1].edgemap)[1] = 0; /* you are on the right edge */ (tmpedge[1].edgemap)[2] = 3; /* go up/down right for leaf 2 */ (tmpedge[2].edgemap)[0] = 1; /* go up for leaf 0 */ (tmpedge[2].edgemap)[1] = 2; /* go up/down left for leaf 1 */ (tmpedge[2].edgemap)[2] = 0; /* you are on the right edge */ #endif (tmpedge[0].split)[0] = 0; /* leaf 0 above this edge */ tmpedge[0].upsize = 1; (tmpedge[0].split)[Maxspc-1] = 1; /* leaf 0 below this edge */ (tmpedge[0].split)[Maxspc-2] = 2; /* leaf 0 below this edge */ tmpedge[0].downsize = 2; (tmpedge[1].split)[0] = 0; /* leaf 0 above this edge */ (tmpedge[1].split)[1] = 2; /* leaf 0 above this edge */ tmpedge[1].upsize = 2; (tmpedge[1].split)[Maxspc-1] = 1; /* leaf 0 below this edge */ tmpedge[1].downsize = 1; (tmpedge[2].split)[0] = 0; /* leaf 0 above this edge */ (tmpedge[2].split)[1] = 1; /* leaf 0 above this edge */ tmpedge[2].upsize = 2; (tmpedge[2].split)[Maxspc-1] = 2; /* leaf 0 below this edge */ tmpedge[2].downsize = 1; /* interconnection */ tmpedge[0].up = NULL; tmpedge[0].downleft = &tmpedge[1]; tmpedge[0].downright = &tmpedge[2]; tmpedge[1].up = &tmpedge[0]; tmpedge[1].downleft = NULL; tmpedge[1].downright = NULL; tmpedge[2].up = &tmpedge[0]; tmpedge[2].downleft = NULL; tmpedge[2].downright = NULL; /* edges of leaves */ tmpedgeofleaf[0] = 0; tmpedgeofleaf[1] = 1; tmpedgeofleaf[2] = 2; } /* inittree */ /******************/ /* add next leaf on the specified edge */ void updatesplit_split(ONEEDGE_SPLIT curredge, /* current edge */ int wherefrom, /* direction to last curr. edge */ int newleaf, /* leaf to add to splits */ ONEEDGE_SPLIT *edge, /* edge array */ int Maxspc, /* No. of species */ int Maxbrnch, /* No. of branches */ int *edgeofleaf, /* ext. edge idx array */ int *in_nextedge, /* next free edge idx */ int *in_nextleaf) /* next free leaf idx */ { int n; switch (wherefrom) { case STARTING: if (curredge.up != NULL) { /* non-root edge */ curredge.split[Maxspc-(++(curredge.upsize))] = newleaf; /* start edge: must be down */ if (((curredge.up)->downright) == &curredge) { updatesplit_split(*(curredge.up), DOWNRIGHT, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } else { updatesplit_split(*(curredge.up), DOWNLEFT, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } } else { /* root -> every thing below/shouldn't happen */ for (n=0; n<*in_nextedge; n++) { edge[n].split[(edge[n].upsize)++] = newleaf; } } break; case UP: curredge.split[(curredge.downsize)++] = newleaf; /* leaf is up */ if (curredge.downright != NULL) { /* not leaf */ updatesplit_split(*(curredge.downright), UP, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); updatesplit_split(*(curredge.downleft), UP, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } else { /* nothing to do */ return; } break; case DOWNLEFT: curredge.split[(curredge.downsize)++] = newleaf; /* leaf is down */ if (curredge.downright != NULL) { /* not leaf */ updatesplit_split(*(curredge.downright), UP, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } if (curredge.up != NULL) { /* not root */ if (((curredge.up)->downright) == &curredge) { updatesplit_split(*(curredge.up), DOWNRIGHT, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } else { updatesplit_split(*(curredge.up), DOWNLEFT, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } } break; case DOWNRIGHT: curredge.split[(curredge.downsize)++] = newleaf; /* leaf is down */ if ((curredge.downright) != NULL) { /* not leaf */ updatesplit_split(*(curredge.downleft), UP, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } if ((curredge.up) != NULL) { /* not root */ if (((curredge.up)->downright) == &curredge) { updatesplit_split(*(curredge.up), DOWNRIGHT, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } else { updatesplit_split(*(curredge.up), DOWNLEFT, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } } break; } } /* addnextleaf_split */ /******************/ /* add next leaf on the specified edge */ void addnextleaf_split(int dockedge, /* insert here */ ONEEDGE_SPLIT *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc, /* No. of species */ int Maxbrnch, /* No. of branches */ int *in_nextedge, /* next free edge idx */ int *in_nextleaf) /* next free leaf idx */ { int i; int nextedge; int nextleaf; nextedge=*in_nextedge; nextleaf=*in_nextleaf; if (dockedge >= nextedge) { /* Trying to add leaf nextleaf to nonexisting edge dockedge */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR F TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } if (nextleaf >= Maxspc) { /* Trying to add leaf nextleaf to a tree with Maxspc leaves */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR G TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } /* necessary change in edgeofleaf if dockedge == edgeofleaf[0] */ if (edgeofleaf[0] == dockedge) edgeofleaf[0] = nextedge; /* adding nextedge to the tree */ edge[nextedge].up = edge[dockedge].up; edge[nextedge].downleft = &edge[dockedge]; edge[nextedge].downright = &edge[nextedge+1]; edge[dockedge].up = &edge[nextedge]; if (edge[nextedge].up != NULL) { if ( ((edge[nextedge].up)->downleft) == &edge[dockedge] ) (edge[nextedge].up)->downleft = &edge[nextedge]; else (edge[nextedge].up)->downright = &edge[nextedge]; } /* adding nextedge + 1 to the tree */ edge[nextedge+1].up = &edge[nextedge]; edge[nextedge+1].downleft = NULL; edge[nextedge+1].downright = NULL; edgeofleaf[nextleaf] = nextedge+1; #if 0 /* the two new edges get info about the old edges */ /* nextedge */ for (i = 0; i < nextedge; i++) { switch ( (edge[dockedge].edgemap)[i] ) { /* down right changes to down left */ case 5: (edge[nextedge].edgemap)[i] = 4; break; /* null changes to down left */ case 0: (edge[nextedge].edgemap)[i] = 4; break; default:(edge[nextedge].edgemap)[i] = (edge[dockedge].edgemap)[i]; break; } } /* nextedge + 1 */ for (i = 0; i < nextedge; i++) { switch ( (edge[dockedge].edgemap)[i] ) { /* up/down left changes to up */ case 2: (edge[nextedge+1].edgemap)[i] = 1; break; /* up/down right changes to up */ case 3: (edge[nextedge+1].edgemap)[i] = 1; break; /* down left changes to up/down left */ case 4: (edge[nextedge+1].edgemap)[i] = 2; break; /* down right changes to up/down left */ case 5: (edge[nextedge+1].edgemap)[i] = 2; break; /* null changes to up/down left */ case 0: (edge[nextedge+1].edgemap)[i] = 2; break; /* up stays up */ default:(edge[nextedge+1].edgemap)[i] = (edge[dockedge].edgemap)[i]; break; } } /* dockedge */ for (i = 0; i < nextedge; i++) { switch ( (edge[dockedge].edgemap)[i] ) { /* up/down right changes to up */ case 3: (edge[dockedge].edgemap)[i] = 1; break; /* up/down left changes to up */ case 2: (edge[dockedge].edgemap)[i] = 1; break; default: break; } } /* all edgemaps are updated for the two new edges */ /* nextedge */ (edge[nextedge].edgemap)[nextedge] = 0; (edge[nextedge].edgemap)[nextedge+1] = 5; /* down right */ /* nextedge + 1 */ (edge[nextedge+1].edgemap)[nextedge] = 1; /* up */ (edge[nextedge+1].edgemap)[nextedge+1] = 0; /* all other edges */ for (i = 0; i < nextedge; i++) { (edge[i].edgemap)[nextedge] = (edge[i].edgemap)[dockedge]; (edge[i].edgemap)[nextedge+1] = (edge[i].edgemap)[dockedge]; } /* an extra for dockedge */ (edge[dockedge].edgemap)[nextedge] = 1; /* up */ (edge[dockedge].edgemap)[nextedge+1] = 3; /* up/down right */ #endif nextleaf++; nextedge = nextedge + 2; *in_nextedge=nextedge; *in_nextleaf=nextleaf; } /* addnextleaf */ /******************/ /* free memory (to be called after inittree) */ void freetree_split(ONEEDGE_SPLIT *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc) /* No. of species */ { int i; for (i = 0; i < 2 * Maxspc - 3; i++) free(edge[i].split); free(edge); free(edgeofleaf); } /* freetree */ /******************/ /* trueID (HAS) */ /* writes OTU sitting on edge ed */ void writeOTU_split(FILE *outfp, /* output file */ int ed, /* edge to subtree */ ONEEDGE_SPLIT *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *column, /* current screen depth */ int *trueID) /* species permutation */ { int i; /* test whether we are on a leaf */ if (edge[ed].downright == NULL && edge[ed].downleft == NULL) { for (i = 1; i < nextleaf; i++) { if (edgeofleaf[i] == ed) { /* i is the leaf of ed */ *column += fputid(outfp, trueID[i]); return; } } } /* we are NOT on a leaf */ fprintf(outfp, "("); (*column)++; writeOTU_split(outfp, edge[ed].downleft->numedge, edge, edgeofleaf, nextedge, nextleaf, column, trueID); fprintf(outfp, ","); (*column)++; (*column)++; if (*column > 55) { *column = 2; fprintf(outfp, "\n "); } writeOTU_split(outfp, edge[ed].downright->numedge, edge, edgeofleaf, nextedge, nextleaf, column, trueID); fprintf(outfp, ")"); (*column)++; } /* writeOTU */ /******************/ /* trueID (HAS) */ /* write tree */ void writetree_split(FILE *outfp, /* output file */ ONEEDGE_SPLIT *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *trueID) /* species permutation */ { int column; column = 1; fprintf(outfp, "("); column += fputid(outfp, trueID[0]) + 3; fprintf(outfp, ","); writeOTU_split(outfp, edge[edgeofleaf[0]].downleft->numedge, edge, edgeofleaf, nextedge, nextleaf, &column, trueID); column++; column++; fprintf(outfp, ","); writeOTU_split(outfp, edge[edgeofleaf[0]].downright->numedge, edge, edgeofleaf, nextedge, nextleaf, &column, trueID); fprintf(outfp, ");\n"); } /* writetree */ /******************/ /* clear all edgeinfos */ void resetedgeinfo_split(ONEEDGE_SPLIT *edge, /* edge array */ int nextedge) /* next free edge idx */ { int i; for (i = 0; i < nextedge; i++) edge[i].penalty = 0; } /* resetedgeinfo */ #if 0 /******************/ /* increment all edgeinfo between leaf A and B */ void incrementedgeinfo_split(int A, /* start leaf of penalty path */ int B, /* start leaf of penalty path */ ONEEDGE_SPLIT *edge, /* edge array */ int *edgeofleaf) /* ext. edge idx array */ { int curredge, finaledge, nextstep; if (A == B) return; finaledge = edgeofleaf[B]; curredge = edgeofleaf[A]; edge[curredge].penalty = edge[curredge].penalty + 1; while (curredge != finaledge) { nextstep = (edge[curredge].edgemap)[finaledge]; switch (nextstep) { /* up */ case 1: curredge = (edge[curredge].up)->numedge; break; /* up/down left */ case 2: curredge = ((edge[curredge].up)->downleft)->numedge; break; /* up/down right */ case 3: curredge = ((edge[curredge].up)->downright)->numedge; break; /* down left */ case 4: curredge = (edge[curredge].downleft)->numedge; break; /* down right */ case 5: curredge = (edge[curredge].downright)->numedge; break; } edge[curredge].edgeinfo = edge[curredge].edgeinfo + 1; } } /* incrementedgeinfo */ #endif /******************/ /* checks which edge has the lowest edgeinfo if there are several edges with the same lowest edgeinfo, one of them will be selected randomly */ void minimumedgeinfo_split(ONEEDGE_SPLIT *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *out_minedge, /* minimum edge set */ uli *out_mininfo) /* minumum penalty */ { int i, k, howmany, randomnum; int minedge; /* minimum edge set */ uli mininfo; /* minumum penalty */ howmany = 1; minedge = 0; mininfo = edge[0].penalty; for (i = 1; i < nextedge; i++) if (edge[i].penalty <= mininfo) { if (edge[i].penalty == mininfo) { howmany++; } else { minedge = i; mininfo = edge[i].penalty; howmany = 1; } } if (howmany > 1) { /* draw random edge */ randomnum = randominteger(howmany) + 1; /* 1 to howmany */ i = -1; for (k = 0; k < randomnum; k++) { do { i++; } while (edge[i].penalty != mininfo); minedge = i; } } *out_minedge=minedge; *out_mininfo=mininfo; } /* minimumedgeinfo */ /*************************************************************************/ /* global functions of the puzzling step */ /*************************************************************************/ /* trueID (HAS) */ /* perform one single puzzling step to produce one intermediate tree */ void onepstep_split( /* PStep (intermediate) tree topol: */ ONEEDGE_SPLIT **edge, /* out: new array of edges */ int **edgeofleaf, /* out: array of extern edge ptrs */ unsigned char *quartettopols, /* in: quartetblock with all topols */ int Maxspc, /* in: Number of species (n) */ ivector permutation) /* in: species permutation (trueID) */ { int Maxbrnch = (2*Maxspc)-3; /* Number of branches (2n-3) */ int nextedge; /* next free edge index (=3) */ int nextleaf; /* next free leaf index (=3) */ int minedge; /* insertion edge of minimum penalty */ uli mininfo; /* minimum penalty */ int a, b, c, i; /* quartet leaves, i to be inserted */ int chooseX, chooseY; /* end leaves of penalty path */ /* allocate and initialize new tree topology */ inittree_split(edge, edgeofleaf, Maxspc, Maxbrnch, &nextedge, &nextleaf); /* adding all other leafs */ for (i = 3; i < Maxspc; i++) { /* clear all edgeinfos */ resetedgeinfo_split(*edge, nextedge); /* * core of quartet puzzling algorithm */ for (a = 0; a < nextleaf - 2; a++) for (b = a + 1; b < nextleaf - 1; b++) for (c = b + 1; c < nextleaf; c++) { /* check which two leaves out of a,b,c are closer related to each other than to leaf i according to a least squares fit of the continous Bayesian weights to the seven trivial "attractive regions". We assign a score of 1 to all edges on the penalty path between these two leaves chooseX and chooseY */ /* trueID (HAS) */ checkquartet_trueID(a, b, c, i, permutation, &chooseX, &chooseY); incrementedgeinfo_split(chooseX, chooseY, *edge, *edgeofleaf); } /* for all quartets q=(a,b,c,i) */ /* find out which edge has lowest edgeinfo */ minimumedgeinfo_split(*edge, *edgeofleaf, nextedge, nextleaf, &minedge, &mininfo); /* add the next leaf on minedge */ addnextleaf_split(minedge, *edge, *edgeofleaf, Maxspc, Maxbrnch, &nextedge, &nextleaf); } /* adding all other leafs */ } /* onepstep_split */ /*************************************************************************/ /* perform Numtrial single puzzling steps constructing Numtrial intermediate */ /* trees, sort each of them and extract splits for consensus step */ void allpstep_split(uli Numtrial, /* in: no. psteps to perform */ unsigned char *quartetinfo, /* in: quartetblock with all topols*/ int Maxspc, /* in: Number of species (n) */ int fixedorder_optn) /* in: 'fixed' anchored RNG (debug)*/ { /* misc variables */ /* trueID (HAS) */ ivector trueIDtmp; /* species permutation (trueID) */ uli Currtrial; /* step counter */ /* PStep (intermediate) tree topol: */ ONEEDGE_SPLIT *tmpedgeset; /* array of edges */ int *tmpedgeofleaf; /* array of extern edge pointers */ /* for unique sorting of tree topologies */ int *ctree; /* sort tree */ int startnode; /* root in sort tree */ char *trstr; /* phylip tree string */ treelistitemtype *treeitem; /* list entry of tree */ # if PARALLEL cmatrix *bp; /* temporary buffer for splits in slaves */ int n; /* step count for init/free split buffer */ # endif /* PARALLEL */ # if PARALLEL /* add times to arry */ addtimes(GENERAL, &tarr); /* alloc temporary split memory */ bp = (cmatrix *) calloc((size_t) Numtrial, sizeof(void *)); for(n=0; n phylip tree string */ trstr=sprintfctree(ctree, psteptreestrlen); /* add sorted tree to unique tree list */ treeitem = addtree2list(&trstr, 1, &psteptreelist, &psteptreenum, &psteptreesum); # if ! PARALLEL /* output unique tree to trace list, if option set */ /* not done on slave processes */ if((listqptrees == PSTOUT_LIST) || (listqptrees == PSTOUT_LISTORDER)) { /* print: order no/# topol per this id/tree id/sum of unique topologies/sum of trees so far */ fprintf(qptlist, "%ld.\t1\t%d\t%d\t%d\t%d\n", Currtrial + 1, (*treeitem).count, (*treeitem).id, psteptreenum, psteptreesum); } # endif /* ! PARALLEL */ # ifdef VERBOSE1 printf("%s\n", trstr); printfsortedpstrees(psteptreelist); # endif /* free sorting tree structure */ freectree(&ctree); /* free tree before building the next tree */ freetree_split(tmpedgeset, tmpedgeofleaf, Maxspc); # if ! PARALLEL /* generate message roughly every 15 minutes */ /* check timer */ time(&time2); if ( (time2 - time1) > TIMECHECK_INTERVAL) { double tc2, mintogo, minutes, hours; /* every TIMECHECK_INTERVAL seconds */ /* percentage of completed trees */ if (mflag == 0) { fprintf(STDOUT, "\n"); mflag = 1; } tc2 = 100.0*Currtrial/Numtrial; /* excluded for less runtime, but less accuracy of the 15min */ /* + 100.0*nq/Numquartets/Numtrial; */ mintogo = (100.0-tc2) * (double) (time2-time0)/60.0/tc2; hours = floor(mintogo/60.0); minutes = mintogo - 60.0*hours; fprintf(STDOUT, "%2.2f%%", tc2); fprintf(STDOUT, " completed (remaining"); fprintf(STDOUT, " time: %.0f", hours); fprintf(STDOUT, " hours %.0f", minutes); fprintf(STDOUT, " minutes)\n"); fflush(STDOUT); time1 = time2; } /* check timer */ # endif /* ! PARALLEL */ addtimes(PUZZLING, &tarr); } /* for Numtrials */ # if PARALLEL /* in slaves: send results: splits, trees */ PP_SendSplitsBlock(Maxspc, Numtrial, bp, psteptreenum, psteptreelist); /* free temporary split memory */ for (Currtrial = 0; Currtrial < Numtrial; Currtrial++) { free_cmatrix(bp[Currtrial]); } free(bp); /* sent! Thus, in slave process not needed any more */ freetreelist(&psteptreelist, &psteptreenum, &psteptreesum); # endif /* PARALLEL */ } /* allpstep_split */ tree-puzzle-5.2/src/pstep-split.h0000644000076400001440000001714510073365265012572 /* * pstep-split.h * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ /* split based O(n^4) algorithm */ #ifndef PSTEP_SPLIT_H #define PSTEP_SPLIT_H #include #include #include"puzzle.h" #include"util.h" /* #include"newpstep.h" */ #ifndef ONEEDGE # define ONEEDGE ONEEDGE_SPLIT #endif /* ! ONEEDGE_DEFINED */ #define NOWHERE 0 #define UP 1 #define UPDOWNLEFT 2 #define UPDOWNRIGHT 3 #define DOWNLEFT 4 #define DOWNRIGHT 5 #define STARTING 6 /* tree structure */ typedef struct oneedge_split { /* pointer to other three edges */ struct oneedge_split *up; struct oneedge_split *downleft; struct oneedge_split *downright; int numedge; /* number of edge (index) */ uli penalty; /* penalty of this edge */ int *split; /* cluster array (up: 0..upsize-1; down: maxspc-1..maxspc-downsize */ int upsize; /* size of root-ward cluster */ int downsize; /* size of non-root-ward cluster */ #if 0 uli edgeinfo; /* value of this edge (penalty) */ int *edgemap; /* _orig algorithm: pointer to the local edgemap array */ int *upcluster; /* cluster array of root-ward taxa */ int *downcluster; /* cluster array of non-root-ward taxa */ #endif } ONEEDGE_SPLIT; /*****************************************************************************/ /* internal functions for representing and building puzzling step trees */ /*****************************************************************************/ /* initialize tree with the following starting configuration * * 2 * 0 +------- C(=2) * A(=0) -----+ * +------- B(=1) * 1 * * * A(=0) * [up =NULL] * [downleft =1] * [downright=2] * [upcluster=0] * [downcluster=1,2] * [upsize=1] * [downsize=2] * * o * | * | * +-------------+--------------+ * | | * | | * o o * * C(=1) B(=2) * [up =0] [up =0] * [downleft =NULL] [downleft =NULL] * [downright=NULL] [downright=NULL] * [upcluster=0,2] [upcluster=0] * [downcluster=1] [downcluster=2] * [upsize=2] [upsize=2] * [downsize=1] [downsize=1] * * nextedge = 3 * nextleaf = 3 * and set according edge maps * */ void inittree_split(ONEEDGE_SPLIT **edge, /* out: new array of edges */ int **edgeofleaf,/* out: array of external edge ptrs */ int Maxspc, /* in: Number of species (n) */ int Maxbrnch, /* in: Number of branches (2n-3) */ int *nextedge, /* out: next free edge index (=3) */ int *nextleaf); /* out: next free leaf index (=3) */ /* add next leaf on the specified edge */ void addnextleaf_split(int dockedge, /* insert here */ ONEEDGE_SPLIT *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc, /* No. of species */ int Maxbrnch, /* No. of branches */ int *nextedge, /* next free edge idx */ int *nextleaf); /* next free leaf idx */ /* free memory (to be called after inittree) */ void freetree_split(ONEEDGE_SPLIT *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc); /* No. of species */ /* writes OTU sitting on edge ed */ void writeOTU_split(FILE *outfp, /* output file */ int ed, /* edge to subtree */ ONEEDGE_SPLIT *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *column, /* current screen depth */ int *trueID); /* species permutation */ /* write tree */ void writetree_split(FILE *outfp, /* output file */ ONEEDGE_SPLIT *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *trueID); /* species permutation */ /* clear all edgeinfos */ void resetedgeinfo_split(ONEEDGE_SPLIT *edge, /* edge array */ int nextedge); /* next free edge idx */ /* increment all edgeinfo between leaf A and B */ void incrementedgeinfo_split(int A, /* start leaf of penalty path */ int B, /* start leaf of penalty path */ ONEEDGE_SPLIT *edge, /* edge array */ int *edgeofleaf); /* ext. edge idx array */ /* checks which edge has the lowest edgeinfo if there are several edges with the same lowest edgeinfo, one of them will be selected randomly */ void minimumedgeinfo_split(ONEEDGE_SPLIT *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *minedge, /* minimum edge set */ uli *mininfo); /* minumum penalty */ /*****************************************************************************/ /* global functions for representing and building puzzling step trees */ /*****************************************************************************/ /* perform one single puzzling step to produce one intermediate tree */ void onepstep_split( /* PStep (intermediate) tree topol: */ ONEEDGE_SPLIT **edge, /* out: new array of edges */ int **edgeofleaf, /* out: array of extern edge ptrs */ unsigned char *quartettopols, /* in: quartetblock with all topols */ int Maxspc, /* in: Number of species (n) */ ivector permutation); /* in: species permutation (trueID) */ /* perform Numtrial single puzzling steps constructing Numtrial intermediate */ /* trees, sort each of them and extract splits for consensus step */ void allpstep_split(uli Numtrial, /* in: no. psteps to perform */ unsigned char *quartetinfo, /* in: quartetblock with all topols*/ int Maxspc, /* in: Number of species (n) */ int fixedorder_optn); /* in: 'fixed' anchored RNG (debug)*/ #endif /* PSTEP_SPLIT_H */ tree-puzzle-5.2/src/model1.c0000644000076400001440000002153210073365272011453 /* * model1.c * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifdef HAVE_CONFIG_H # include #endif /* definitions */ #define EXTERN extern /* prototypes */ #include #include "util.h" #include "puzzle.h" #include "ml.h" /* number of states of the selected model */ int gettpmradix() { if (data_optn == 0) { /* nucleotides */ if (nuc_optn) return 4; if (SH_optn) return 16; } else if (data_optn == 1) { /* amino acids */ return 20; } else { /* two-state model */ return 2; } return 1; } /* gettpmradix */ /* relative transition frequencies */ void rtfdata(dmatrix q, double *f) { double alp, alpy, alpr; int i, j; if (data_optn == 0) { /* nucleotides */ if (nuc_optn) { /* 4x4 nucleotides */ if (!GTR_optn) { alp = 2.0*TSparam; alpr = (alp * 2.0) / (YRparam + 1.0); alpy = YRparam * alpr; q[0][1] =1; q[0][2] =alpr; q[0][3] =1; q[1][2] =1; q[1][3] =alpy; q[2][3] =1; GTR_ACrate = q[0][1]; GTR_AGrate = q[0][2]; GTR_ATrate = q[0][3]; GTR_CGrate = q[1][2]; GTR_CTrate = q[1][3]; GTR_GTrate = q[2][3]; f[0] = 0.25; f[1] = 0.25; f[2] = 0.25; f[3] = 0.25; } else { #if 0 alp = 2.0*TSparam; alpr = (alp * 2.0) / (YRparam + 1.0); alpy = YRparam * alpr; #endif q[0][1] = GTR_ACrate; q[0][2] = GTR_AGrate; q[0][3] = GTR_ATrate; q[1][2] = GTR_CGrate; q[1][3] = GTR_CTrate; q[2][3] = GTR_GTrate; f[0] = 0.25; f[1] = 0.25; f[2] = 0.25; f[3] = 0.25; } } if (SH_optn) { /* 16x16 nucleotides */ alp = 2.0*TSparam; q[0][1] =1; q[0][2] =alp; q[0][3] =1; q[0][4] =1; q[0][5] =0; q[0][6] =0; q[0][7] =0; q[0][8] =alp; q[0][9] =0; q[0][10] =0; q[0][11] =0; q[0][12] =1; q[0][13] =0; q[0][14] =0; q[0][15] =0; q[1][2] =1; q[1][3] =alp; q[1][4] =0; q[1][5] =1; q[1][6] =0; q[1][7] =0; q[1][8] =0; q[1][9] =alp; q[1][10] =0; q[1][11] =0; q[1][12] =0; q[1][13] =1; q[1][14] =0; q[1][15] =0; q[2][3] =1; q[2][4] =0; q[2][5] =0; q[2][6] =1; q[2][7] =0; q[2][8] =0; q[2][9] =0; q[2][10] =alp; q[2][11] =0; q[2][12] =0; q[2][13] =0; q[2][14] =1; q[2][15] =0; q[3][4] =0; q[3][5] =0; q[3][6] =0; q[3][7] =1; q[3][8] =0; q[3][9] =0; q[3][10] =0; q[3][11] =alp; q[3][12] =0; q[3][13] =0; q[3][14] =0; q[3][15] =1; q[4][5] =1; q[4][6] =alp; q[4][7] =1; q[4][8] =1; q[4][9] =0; q[4][10] =0; q[4][11] =0; q[4][12] =alp; q[4][13] =0; q[4][14] =0; q[4][15] =0; q[5][6] =1; q[5][7] =alp; q[5][8] =0; q[5][9] =1; q[5][10] =0; q[5][11] =0; q[5][12] =0; q[5][13] =alp; q[5][14] =0; q[5][15] =0; q[6][7] =1; q[6][8] =0; q[6][9] =0; q[6][10] =1; q[6][11] =0; q[6][12] =0; q[6][13] =0; q[6][14] =alp; q[6][15] =0; q[7][8] =0; q[7][9] =0; q[7][10] =0; q[7][11] =1; q[7][12] =0; q[7][13] =0; q[7][14] =0; q[7][15] =alp; q[8][9] =1; q[8][10] =alp; q[8][11] =1; q[8][12] =1; q[8][13] =0; q[8][14] =0; q[8][15] =0; q[9][10] =1; q[9][11] =alp; q[9][12] =0; q[9][13] =1; q[9][14] =0; q[9][15] =0; q[10][11]=1; q[10][12]=0; q[10][13]=0; q[10][14]=1; q[10][15]=0; q[11][12]=0; q[11][13]=0; q[11][14]=0; q[11][15]=1; q[12][13]=1; q[12][14]=alp; q[12][15]=1; q[13][14]=1; q[13][15]=alp; q[14][15]=1; for (i = 0; i < 16; i++) f[i] = 0.0625; } } else if (data_optn == 1) { /* amino acids */ if (Dayhf_optn) /* Dayhoff model */ { dyhfdata(q, f); } else if (Jtt_optn) /* JTT model */ { jttdata(q, f); } else if (blosum62_optn) /* BLOSUM 62 model */ { blosum62data(q, f); } else if (mtrev_optn) /* mtREV model */ { mtrevdata(q, f); } else if (cprev_optn) /* cpREV model */ { cprev45data(q, f); } else if (vtmv_optn) /* VT model */ { vtmvdata(q, f); } else /* if (wag_optn) */ /* WAG model */ { wagdata(q, f); } } else /* two-state model */ { q[0][1] = 1.0; f[0] = 0.5; f[1] = 0.5; } /* fill matrix from upper triangle */ for (i = 0; i < tpmradix; i++) { q[i][i] = 0.0; for (j = i+1; j < tpmradix; j++) { q[j][i] = q[i][j]; } } } /* rtfdata */ /* transform letter codes to state numbers */ int code2int(cvector c, int *numgaps, int *others) { if (data_optn == NUCLEOTIDE) { /* nucleotides */ if (nuc_optn) { /* 4x4 */ switch (c[0]) { case 'A': return 0; case 'C': return 1; case 'G': return 2; case 'T': return 3; case 'U': return 3; case '-': (*numgaps)++; return 4; default : (*others)++; return 4; } } /* nuc - 4x4 */ if (SH_optn) { /* 16x16 */ if (c[0] == 'A') { switch (c[1]) { case 'A': return 0; /* AA */ case 'C': return 1; /* AC */ case 'G': return 2; /* AG */ case 'T': return 3; /* AT */ case 'U': return 3; /* AT */ case '-': (*numgaps)++; return 16; /* A- */ default: (*others)++; return 16; } } if (c[0] == 'C') { switch (c[1]) { case 'A': return 4; /* CA */ case 'C': return 5; /* CC */ case 'G': return 6; /* CG */ case 'T': return 7; /* CT */ case 'U': return 7; /* CT */ case '-': (*numgaps)++; return 16; /* C- */ default: (*others)++; return 16; } } if (c[0] == 'G') { switch (c[1]) { case 'A': return 8; /* GA */ case 'C': return 9; /* GC */ case 'G': return 10; /* GG */ case 'T': return 11; /* GT */ case 'U': return 11; /* GT */ case '-': (*numgaps)++; return 16; /* G- */ default: (*others)++; return 16; } } if (c[0] == 'T' || c[0] == 'U') { switch (c[1]) { case 'A': return 12; /* TA */ case 'C': return 13; /* TC */ case 'G': return 14; /* TG */ case 'T': return 15; /* TT */ case 'U': return 15; /* TT */ case '-': (*numgaps)++; return 16; /* T- */ default: (*others)++; return 16; } } /* -A, -C, -G, -T, ?A, ?C, ?G, ?T */ if (c[0] == '-') (*numgaps)++; else (*others)++; if (!((c[1] == 'T') || (c[1] == 'U') || (c[1] == 'T') || (c[1] == 'U'))) { if (c[1] == '-') (*numgaps)++; else (*others)++; } return 16; } /* SH - 16x16 */ } else if (data_optn == AMINOACID) { /* amino acids */ switch (c[0]) { case 'A': return 0; case 'C': return 4; case 'D': return 3; case 'E': return 6; case 'F': return 13; case 'G': return 7; case 'H': return 8; case 'I': return 9; case 'K': return 11; case 'L': return 10; case 'M': return 12; case 'N': return 2; case 'P': return 14; case 'Q': return 5; case 'R': return 1; case 'S': return 15; case 'T': return 16; case 'V': return 19; case 'W': return 17; case 'Y': return 18; case '-': (*numgaps)++; return 20; default : (*others)++; return 20; } } else { /* two-state model - BINARY */ switch (c[0]) { case '0': return 0; case '1': return 1; case '-': (*numgaps)++; return 2; default : (*others)++; return 2; } } /* two-state model */ return 0; } /* code2int */ /* return letter code belonging to state number */ char *int2code(int s) { if (data_optn == 0) { /* nucleotides */ if (nuc_optn) { /* 4x4 */ switch (s) { case 0: return "A"; case 1: return "C"; case 2: return "G"; case 3: return "T"; default : return "?"; } } if (SH_optn) { /* 16x16 */ switch (s) { case 0: return "AA"; case 1: return "AC"; case 2: return "AG"; case 3: return "AT"; case 4: return "CA"; case 5: return "CC"; case 6: return "CG"; case 7: return "CT"; case 8: return "GA"; case 9: return "GC"; case 10: return "GG"; case 11: return "GT"; case 12: return "TA"; case 13: return "TC"; case 14: return "TG"; case 15: return "TT"; default : return "??"; } } } else if (data_optn == 1) { /* amino acids */ switch (s) { case 0: return "A"; case 1: return "R"; case 2: return "N"; case 3: return "D"; case 4: return "C"; case 5: return "Q"; case 6: return "E"; case 7: return "G"; case 8: return "H"; case 9: return "I"; case 10: return "L"; case 11: return "K"; case 12: return "M"; case 13: return "F"; case 14: return "P"; case 15: return "S"; case 16: return "T"; case 17: return "W"; case 18: return "Y"; case 19: return "V"; default : return "?"; } } else { /* two-state model */ switch (s) { case 0: return "0"; case 1: return "1"; default : return "?"; } } return "?"; } /* int2code */ tree-puzzle-5.2/src/model2.c0000644000076400001440000013725110073365276011466 /* * model2.c * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifdef HAVE_CONFIG_H # include #endif /* definitions */ #define EXTERN extern /* prototypes */ #include #include "util.h" #include "ml.h" /* IUPAC AA Codings: * * ordered by 1-letter-code: * * A C D E F G H I K L M N P Q R S T V W Y -/others * Ala Cys Asp Glu Phe Gly His Ile Lys Leu Met Asn Pro Gln Arg Ser Thr Val Trp Tyr * 0 4 3 6 13 7 8 9 11 10 12 2 14 5 1 15 16 19 17 18 20 * * * ordered by 3-letter-code/index: * * 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 * A R N D C Q E G H I L K M F P S T W Y V -/others * Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val * */ void jttdata(dmatrix q, double *f) { /* * JTT model for amino acid evolution * D.T. Jones, W.R. Taylor, and J.M. Thornton * "The rapid generation of mutation data matrices from protein sequences" * CABIOS vol. 8 no. 3 1992 pp. 275-282 */ q[0][1]=3.1628651460584e+00; q[0][2]=3.2804935927860e+00; q[0][3]=4.8477237048666e+00; q[0][4]=3.4612244897959e+00; q[0][5]=3.3130910900946e+00; q[0][6]=6.3199473337722e+00; q[0][7]=1.0440154440154e+01; q[0][8]=1.3061224489796e+00; q[0][9]=2.1726844583987e+00; q[0][10]=1.8443597219107e+00; q[0][11]=2.2137668626773e+00; q[0][12]=2.7210884353741e+00; q[0][13]=8.3265306122449e-01; q[0][14]=1.1537414965986e+01; q[0][15]=2.2838213546288e+01; q[0][16]=2.7007955724663e+01; q[0][17]=5.1311953352770e-01; q[0][18]=8.3673469387755e-01; q[0][19]=1.7474335188621e+01; q[1][2]=2.6598918637222e+00; q[1][3]=9.1014867485456e-01; q[1][4]=6.1624649859944e+00; q[1][5]=1.8036482885837e+01; q[1][6]=1.8924731182796e+00; q[1][7]=8.1810886516769e+00; q[1][8]=1.9119717452198e+01; q[1][9]=1.4410687351864e+00; q[1][10]=2.2211961707760e+00; q[1][11]=3.9239234676922e+01; q[1][12]=2.5060690943044e+00; q[1][13]=3.9439775910364e-01; q[1][14]=4.1953094963476e+00; q[1][15]=5.9016766126741e+00; q[1][16]=3.8437069743152e+00; q[1][17]=7.6766706682673e+00; q[1][18]=1.4173669467787e+00; q[1][19]=1.0308123249300e+00; q[2][3]=3.2226935854843e+01; q[2][4]=1.8710963455150e+00; q[2][5]=4.5351268130622e+00; q[2][6]=3.3951344979102e+00; q[2][7]=4.5987249708180e+00; q[2][8]=2.3693774375271e+01; q[2][9]=2.9235880398671e+00; q[2][10]=8.0960899565551e-01; q[2][11]=1.5024269384537e+01; q[2][12]=1.9003322259136e+00; q[2][13]=4.3853820598007e-01; q[2][14]=7.1083317047749e-01; q[2][15]=2.9456208772690e+01; q[2][16]=1.3735908553410e+01; q[2][17]=1.6706217370669e-01; q[2][18]=4.1661129568106e+00; q[2][19]=9.7452934662237e-01; q[3][4]=6.2857142857143e-01; q[3][5]=3.0662020905923e+00; q[3][6]=4.5450549450549e+01; q[3][7]=7.5402435402435e+00; q[3][8]=6.0544672718586e+00; q[3][9]=6.8808114961961e-01; q[3][10]=3.6130902064968e-01; q[3][11]=1.6718197057180e+00; q[3][12]=1.0879120879121e+00; q[3][13]=1.9340659340659e-01; q[3][14]=7.3949579831933e-01; q[3][15]=3.4196528109572e+00; q[3][16]=2.4749487800335e+00; q[3][17]=3.4536891679749e-01; q[3][18]=2.6895604395604e+00; q[3][19]=1.8608058608059e+00; q[4][5]=5.5191637630662e-01; q[4][6]=3.2442396313364e-01; q[4][7]=3.3297297297297e+00; q[4][8]=4.3726708074534e+00; q[4][9]=9.1868131868132e-01; q[4][10]=9.9466248037677e-01; q[4][11]=2.9830508474576e-01; q[4][12]=2.4095238095238e+00; q[4][13]=4.1485714285714e+00; q[4][14]=7.3949579831933e-01; q[4][15]=1.2862939958592e+01; q[4][16]=2.8125907990315e+00; q[4][17]=6.8244897959184e+00; q[4][18]=1.2885714285714e+01; q[4][19]=3.7714285714286e+00; q[5][6]=2.0316061593796e+01; q[5][7]=1.3922214897825e+00; q[5][8]=3.3861536130889e+01; q[5][9]=4.7172339855267e-01; q[5][10]=4.2320327755868e+00; q[5][11]=1.7835941652395e+01; q[5][12]=2.6573751451800e+00; q[5][13]=2.7595818815331e-01; q[5][14]=9.4992143198743e+00; q[5][15]=3.2350653941322e+00; q[5][16]=3.0973838067678e+00; q[5][17]=1.0512692882031e+00; q[5][18]=1.5331010452962e+00; q[5][19]=1.0778164924506e+00; q[6][7]=6.6857641051189e+00; q[6][8]=1.4458024443999e+00; q[6][9]=6.7068415455512e-01; q[6][10]=5.7932850559579e-01; q[6][11]=1.0365070686558e+01; q[6][12]=1.0138248847926e+00; q[6][13]=2.6359447004608e-01; q[6][14]=1.1291226167887e+00; q[6][15]=1.8337006611901e+00; q[6][16]=1.9520424900414e+00; q[6][17]=6.9519420671494e-01; q[6][18]=3.8018433179723e-01; q[6][19]=2.7772657450077e+00; q[7][8]=1.2113479939567e+00; q[7][9]=3.2670032670033e-01; q[7][10]=4.1817641817642e-01; q[7][11]=1.6354950592239e+00; q[7][12]=7.6447876447876e-01; q[7][13]=3.0579150579151e-01; q[7][14]=1.2391551215081e+00; q[7][15]=1.1138492529797e+01; q[7][16]=1.8888816176952e+00; q[7][17]=3.3491450634308e+00; q[7][18]=3.1853281853282e-01; q[7][19]=2.8416988416988e+00; q[8][9]=1.0931677018634e+00; q[8][10]=3.2194389461470e+00; q[8][11]=3.1498052426571e+00; q[8][12]=1.9130434782609e+00; q[8][13]=2.7329192546584e+00; q[8][14]=6.7304834977469e+00; q[8][15]=4.3726708074534e+00; q[8][16]=2.8162964522581e+00; q[8][17]=7.8083407275954e-01; q[8][18]=3.5118012422360e+01; q[8][19]=7.2877846790890e-01; q[9][10]=1.4069798333535e+01; q[9][11]=1.2292791953809e+00; q[9][12]=2.8366300366300e+01; q[9][13]=4.7384615384615e+00; q[9][14]=5.8780435251023e-01; q[9][15]=2.4105749323141e+00; q[9][16]=1.5243062022723e+01; q[9][17]=8.2888540031397e-01; q[9][18]=1.8434065934066e+00; q[9][19]=5.7699633699634e+01; q[10][11]=8.8039805231089e-01; q[10][12]=2.2425954997384e+01; q[10][13]=1.5099529042386e+01; q[10][14]=6.2626896912611e+00; q[10][15]=3.4917298022888e+00; q[10][16]=1.6109411169944e+00; q[10][17]=3.2366001345593e+00; q[10][18]=1.4505494505495e+00; q[10][19]=1.0557823129252e+01; q[11][12]=3.6577885391445e+00; q[11][13]=1.4915254237288e-01; q[11][14]=1.2868062479229e+00; q[11][15]=2.8162964522581e+00; q[11][16]=5.7494151926786e+00; q[11][17]=5.4790729851263e-01; q[11][18]=5.3268765133172e-01; q[11][19]=7.4899112187248e-01; q[12][13]=2.5666666666667e+00; q[12][14]=9.4491129785247e-01; q[12][15]=1.6397515527950e+00; q[12][16]=1.2180790960452e+01; q[12][17]=1.1972789115646e+00; q[12][18]=1.1130952380952e+00; q[12][19]=1.7746031746032e+01; q[13][14]=8.8739495798319e-01; q[13][15]=5.6298136645963e+00; q[13][16]=8.3099273607748e-01; q[13][17]=3.3224489795918e+00; q[13][18]=3.3392857142857e+01; q[13][19]=3.6000000000000e+00; q[14][15]=1.6261762676085e+01; q[14][16]=6.8852490148602e+00; q[14][17]=4.2256902761104e-01; q[14][18]=6.7787114845938e-01; q[14][19]=1.2549019607843e+00; q[15][16]=2.7891216619293e+01; q[15][17]=1.8740017746229e+00; q[15][18]=3.7349896480331e+00; q[15][19]=2.4182194616977e+00; q[16][17]=4.8702870978900e-01; q[16][18]=1.1985472154964e+00; q[16][19]=6.7925746569814e+00; q[17][18]=4.6020408163265e+00; q[17][19]=1.4693877551020e+00; q[18][19]=1.0000000000000e+00; f[0] = 0.077; f[1] = 0.051; f[2] = 0.043; f[3] = 0.052; f[4] = 0.02; f[5] = 0.041; f[6] = 0.062; f[7] = 0.074; f[8] = 0.023; f[9] = 0.052; f[10] = 0.091; f[11] = 0.059; f[12] = 0.024; f[13] = 0.04; f[14] = 0.051; f[15] = 0.069; f[16] = 0.059; f[17] = 0.014; f[18] = 0.032; f[19] = 0.066; } /* jttdata */ void dyhfdata(dmatrix q, double *f) { /* * Dayhoff model for amino acid evolution * Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C. (1978) * "A model of evolutionary change in proteins." * Dayhoff, M.O. (ed.) Atlas of Protein Sequence Structur., Vol5, Suppl. 3, * National Biomedical Research Foundation, Washington DC, pp. 345-352. */ q[0][1]=9.6472567159749e-01; q[0][2]=3.5927991886410e+00; q[0][3]=4.3200552414656e+00; q[0][4]=1.3184584178499e+00; q[0][5]=3.2267534963169e+00; q[0][6]=7.0141987829615e+00; q[0][7]=8.5773867857875e+00; q[0][8]=8.1434196396611e-01; q[0][9]=2.3518447453539e+00; q[0][10]=1.4735711728911e+00; q[0][11]=9.3940162271805e-01; q[0][12]=2.5490196078431e+00; q[0][13]=6.5922920892495e-01; q[0][14]=8.9189834148670e+00; q[0][15]=1.4540712836859e+01; q[0][16]=1.3411904595370e+01; q[0][17]=3.8517964118027e-02; q[0][18]=8.7897227856660e-01; q[0][19]=7.4036511156187e+00; q[1][2]=1.1890243902439e+00; q[1][3]=5.9525626545377e-02; q[1][4]=8.4778922655537e-01; q[1][5]=8.8348561504191e+00; q[1][6]=5.5954088952654e-02; q[1][7]=3.1434881434075e-01; q[1][8]=8.4753987678285e+00; q[1][9]=2.2684090115941e+00; q[1][10]=5.5954088952654e-01; q[1][11]=1.6681312769010e+01; q[1][12]=3.1707317073171e+00; q[1][13]=4.8959827833572e-01; q[1][14]=3.6754156468900e+00; q[1][15]=5.4755072760812e+00; q[1][16]=9.6472567159749e-01; q[1][17]=7.5538020086083e+00; q[1][18]=2.7977044476327e-01; q[1][19]=8.6083213773314e-01; q[2][3]=3.2459324155194e+01; q[2][4]=7.3852625416383e-02; q[2][5]=3.7732198142415e+00; q[2][6]=5.3911764705882e+00; q[2][7]=5.0264375413087e+00; q[2][8]=1.9061418685121e+01; q[2][9]=2.7901430842607e+00; q[2][10]=1.2482698961938e+00; q[2][11]=1.1542279411765e+01; q[2][12]=1.9117647058824e-01; q[2][13]=5.0183823529412e-01; q[2][14]=1.5181660899654e+00; q[2][15]=1.7697478991597e+01; q[2][16]=8.3557302231237e+00; q[2][17]=8.6029411764706e-01; q[2][18]=3.4411764705882e+00; q[2][19]=5.7352941176471e-01; q[3][4]=2.5534152404601e-02; q[3][5]=4.8811013767209e+00; q[3][6]=4.0561952440551e+01; q[3][7]=4.4423506911730e+00; q[3][8]=3.0865788117500e+00; q[3][9]=8.5749078239692e-01; q[3][10]=2.5926985518518e-02; q[3][11]=2.5930851063830e+00; q[3][12]=1.1667143483333e-01; q[3][13]=1.2963492759259e-02; q[3][14]=4.7853935065891e-01; q[3][15]=3.4167709637046e+00; q[3][16]=2.3984722282163e+00; q[3][17]=3.2408731898147e-02; q[3][18]=8.1351689612015e-02; q[3][19]=6.3829787234043e-01; q[4][5]=2.1864264103535e-02; q[4][6]=1.4770525083277e-02; q[4][7]=3.9055458751427e-01; q[4][8]=1.0223340673168e+00; q[4][9]=1.5970515970516e+00; q[4][10]=3.9098448749850e-02; q[4][11]=8.0776309049169e-03; q[4][12]=1.4155086538140e-01; q[4][13]=8.6898395721925e-02; q[4][14]=6.8155604487784e-01; q[4][15]=5.8097784568373e+00; q[4][16]=5.9929928084086e-01; q[4][17]=3.4759358288770e-01; q[4][18]=3.4759358288770e+00; q[4][19]=1.7647058823529e+00; q[5][6]=2.5476780185759e+01; q[5][7]=1.0174974779977e+00; q[5][8]=2.1573939173192e+01; q[5][9]=6.5266504894988e-01; q[5][10]=2.6634492806410e+00; q[5][11]=5.5466331269350e+00; q[5][12]=4.0247678018576e+00; q[5][13]=1.8038017885416e-02; q[5][14]=5.5044618466582e+00; q[5][15]=2.0267580716497e+00; q[5][16]=1.9256432155439e+00; q[5][17]=9.6202762055552e-02; q[5][18]=1.0061919504644e-01; q[5][19]=1.2538699690402e+00; q[6][7]=2.8869795109055e+00; q[6][8]=1.5519031141869e+00; q[6][9]=2.1701112877583e+00; q[6][10]=4.0484429065744e-01; q[6][11]=2.9823529411765e+00; q[6][12]=1.0705882352941e+00; q[6][13]=1.9801735189768e-02; q[6][14]=1.7993079584775e+00; q[6][15]=2.8184873949580e+00; q[6][16]=1.2261663286004e+00; q[6][17]=7.3114099162219e-02; q[6][18]=7.6470588235294e-01; q[6][19]=1.3058823529412e+00; q[7][8]=3.7906768788150e-01; q[7][9]=2.3128004846840e-02; q[7][10]=2.5776602775942e-01; q[7][11]=9.6662260409782e-01; q[7][12]=6.0145406477198e-01; q[7][13]=5.4775280898876e-01; q[7][14]=1.2382877804129e+00; q[7][15]=8.2853366065527e+00; q[7][16]=1.1110604644803e+00; q[7][17]=1.2888301387971e-01; q[7][18]=1.7114723586662e-02; q[7][19]=1.9233311302049e+00; q[8][9]=2.7354343963341e-01; q[8][10]=1.5876246692449e+00; q[8][11]=9.6993944636678e-01; q[8][12]=1.2544085640577e-01; q[8][13]=1.6868512110727e+00; q[8][14]=3.3075513942601e+00; q[8][15]=1.2530894710826e+00; q[8][16]=8.1434196396611e-01; q[8][17]=1.0121107266436e+00; q[8][18]=4.4982698961938e+00; q[8][19]=1.5570934256055e+00; q[9][10]=9.2275320303002e+00; q[9][11]=1.6663354531002e+00; q[9][12]=1.1780604133545e+01; q[9][13]=6.9753577106518e+00; q[9][14]=4.2551201720752e-01; q[9][15]=8.8575970928912e-01; q[9][16]=6.8951811852420e+00; q[9][17]=9.8802836705702e-02; q[9][18]=1.3434022257552e+00; q[9][19]=3.1526232114467e+01; q[10][11]=6.5787197231834e-01; q[10][12]=1.8622837370242e+01; q[10][13]=5.6340830449827e+00; q[10][14]=1.1377976796255e+00; q[10][15]=6.1690558576372e-01; q[10][16]=1.2098794893211e+00; q[10][17]=1.7543252595156e+00; q[10][18]=1.0346020761246e+00; q[10][19]=6.2906574394464e+00; q[11][12]=8.6029411764706e+00; q[11][13]=6.6640454965565e-03; q[11][14]=1.2089100346021e+00; q[11][15]=3.4411764705882e+00; q[11][16]=4.9442190669371e+00; q[11][17]=3.4272233982290e-02; q[11][18]=4.7794117647059e-01; q[11][19]=3.7500000000000e-01; q[12][13]=3.2500000000000e+00; q[12][14]=5.9976931949250e-01; q[12][15]=2.1848739495798e+00; q[12][16]=3.6916835699797e+00; q[12][17]=1.6247577591604e-01; q[12][18]=1.1508700794053e-01; q[12][19]=9.0588235294118e+00; q[13][14]=3.9359861591695e-01; q[13][15]=1.6386554621849e+00; q[13][16]=4.9442190669371e-01; q[13][17]=2.8676470588235e+00; q[13][18]=2.4852941176471e+01; q[13][19]=4.4117647058824e-01; q[14][15]=8.6431043005437e+00; q[14][16]=2.8308077795013e+00; q[14][17]=3.5840244687362e-02; q[14][18]=4.3804743506776e-02; q[14][19]=1.7301038062284e+00; q[15][16]=1.9663865546218e+01; q[15][17]=2.7857142857143e+00; q[15][18]=1.2016806722689e+00; q[15][19]=1.0840336134454e+00; q[16][17]=4.2019597219666e-02; q[16][18]=1.5162271805274e+00; q[16][19]=5.6592292089249e+00; q[17][18]=2.2941176470588e+00; q[17][19]=1.2654363316538e-01; q[18][19]=1.0000000000000e+00; f[0] = 0.087; f[1] = 0.041; f[2] = 0.040; f[3] = 0.047; f[4] = 0.033; f[5] = 0.038; f[6] = 0.05; f[7] = 0.089; f[8] = 0.034; f[9] = 0.037; f[10] = 0.085; f[11] = 0.08; f[12] = 0.015; f[13] = 0.04; f[14] = 0.051; f[15] = 0.07; f[16] = 0.058; f[17] = 0.01; f[18] = 0.03; f[19] = 0.065; } /* dyhfdata */ void mtrevdata(dmatrix q, double *f) { /* * mtREV24 model of amino acid evolution * (complete sequence data of mtDNA from 24 vertebrate species) * Adachi, J. and Hasegawa, M. (1996) * * (values optained from molphy. matrix normalized such that * sum of lower triangular is 100000 and lower limit is 10.) */ q[0][1] =1.2199217606346e+01; q[0][2] =1.4182139942122e+01; q[0][3] =9.2985091873208e+00; q[0][4] =3.1542792981957e+01; q[0][5] =1.0025852846688e+00; q[0][6] =5.1418866803338e+00; q[0][7] =6.3531246495131e+01; q[0][8] =7.3137132861715e+00; q[0][9] =5.0782382656186e+01; q[0][10] =1.3399741808481e+01; q[0][11] =4.4021672780560e+00; q[0][12] =7.4673480520104e+01; q[0][13] =3.3513021631978e+00; q[0][14] =2.8582502221773e+01; q[0][15] =2.0413623195312e+02; q[0][16] =2.5301305153906e+02; q[0][17] =1.0000000000000e+00; q[0][18] =3.4084158197615e+00; q[0][19] =1.0266468401249e+02; q[1][2] =6.9661274444534e+00; q[1][3] =1.0000000000000e+00; q[1][4] =5.4384584796568e+01; q[1][5] =1.1631134513343e+02; q[1][6] =1.0000000000000e+00; q[1][7] =1.2122831341194e+01; q[1][8] =8.6961067087353e+01; q[1][9] =1.0000000000000e+00; q[1][10] =8.1976829394538e+00; q[1][11] =7.4423215395318e+01; q[1][12] =1.0000000000000e+00; q[1][13] =2.4659158338099e+00; q[1][14] =1.2439947713615e+01; q[1][15] =3.1791814866372e+00; q[1][16] =1.0935327216119e+00; q[1][17] =1.1550775790126e+01; q[1][18] =1.0000000000000e+00; q[1][19] =4.0211417480338e+00; q[2][3] =4.1809325468160e+02; q[2][4] =3.1020979842967e+01; q[2][5] =9.1349622725361e+01; q[2][6] =3.3185663516310e+01; q[2][7] =2.8052324651124e+01; q[2][8] =2.6112087577885e+02; q[2][9] =1.4261453863336e+01; q[2][10] =7.9775653461977e+00; q[2][11] =3.2036829276162e+02; q[2][12] =3.4424354918739e+01; q[2][13] =7.9996445145608e+00; q[2][14] =3.8586541461044e+01; q[2][15] =2.6020426225852e+02; q[2][16] =1.2550758780474e+02; q[2][17] =5.6207759736659e+00; q[2][18] =1.0071406219571e+02; q[2][19] =1.0000000000000e+00; q[3][4] =1.0000000000000e+00; q[3][5] =2.9097352675564e+01; q[3][6] =3.0713149855302e+02; q[3][7] =2.9877072751897e+01; q[3][8] =5.9995408885817e+01; q[3][9] =2.2827096245105e+00; q[3][10] =1.0000000000000e+00; q[3][11] =1.2183938185384e+00; q[3][12] =1.0000000000000e+00; q[3][13] =2.6221929413096e+00; q[3][14] =7.0708004204733e+00; q[3][15] =3.6327934317139e+01; q[3][16] =1.4743408713748e+01; q[3][17] =1.0453246057102e+01; q[3][18] =1.1165627147496e+01; q[3][19] =1.0000000000000e+00; q[4][5] =3.9599394038972e+01; q[4][6] =1.0000000000000e+00; q[4][7] =1.6163581056674e+01; q[4][8] =7.4467985406234e+01; q[4][9] =3.3018175376623e+01; q[4][10] =1.3500725995091e+01; q[4][11] =1.0000000000000e+00; q[4][12] =3.2504095376923e+00; q[4][13] =3.7264767083096e+01; q[4][14] =1.6454136037822e+01; q[4][15] =1.4581783243113e+02; q[4][16] =9.4720031458442e+01; q[4][17] =1.7684087896962e+01; q[4][18] =1.3409157685926e+02; q[4][19] =1.0000000000000e+00; q[5][6] =1.6503249008836e+02; q[5][7] =3.5530760735494e+00; q[5][8] =3.0652523140859e+02; q[5][9] =4.3905393139325e+00; q[5][10] =2.0895470525345e+01; q[5][11] =2.4504076430724e+02; q[5][12] =2.4931300477797e+01; q[5][13] =1.0059428264289e+01; q[5][14] =7.2256314165467e+01; q[5][15] =2.8480937892158e+01; q[5][16] =4.9962974409828e+01; q[5][17] =1.0000000000000e+00; q[5][18] =2.0430790980529e+01; q[5][19] =9.9986289000676e+00; q[6][7] =1.4884496769963e+01; q[6][8] =2.5853576435567e+01; q[6][9] =1.7418201388328e+00; q[6][10] =1.0000000000000e+00; q[6][11] =1.6519126809071e+02; q[6][12] =1.0000000000000e+00; q[6][13] =1.4067850525292e+00; q[6][14] =6.7547121641947e+00; q[6][15] =2.8794794140840e+01; q[6][16] =7.8001372062558e+00; q[6][17] =1.0000000000000e+00; q[6][18] =6.9067239183061e+00; q[6][19] =1.1127702362585e+01; q[7][8] =1.0000000000000e+00; q[7][9] =3.1466649021550e+00; q[7][10] =1.2699794194865e+00; q[7][11] =1.1962111069278e+01; q[7][12] =1.0000000000000e+00; q[7][13] =1.0000000000000e+00; q[7][14] =1.0000000000000e+00; q[7][15] =6.6277950574411e+01; q[7][16] =5.8800079133028e+00; q[7][17] =5.7494182626674e+00; q[7][18] =1.6887657206208e+00; q[7][19] =1.3320553471351e+00; q[8][9] =6.4536986087271e+00; q[8][10] =6.0472584534958e+00; q[8][11] =6.7197196398961e+01; q[8][12] =6.2977633277779e+00; q[8][13] =2.5347805183364e+01; q[8][14] =3.2089868698728e+01; q[8][15] =4.0766987134407e+01; q[8][16] =2.3570850628539e+01; q[8][17] =3.7286635325194e+00; q[8][18] =3.5270764890474e+02; q[8][19] =1.0000000000000e+00; q[9][10] =1.7320653206333e+02; q[9][11] =1.0298655619743e+01; q[9][12] =2.7262244199514e+02; q[9][13] =4.4561065036310e+01; q[9][14] =1.0856482766156e+01; q[9][15] =2.5107659603898e+01; q[9][16] =1.9391167162525e+02; q[9][17] =1.0000000000000e+00; q[9][18] =1.3161329199391e+01; q[9][19] =6.4365086389428e+02; q[10][11]=7.8314019154706e+00; q[10][12]=2.8290920517725e+02; q[10][13]=1.1371735519833e+02; q[10][14]=2.1105885757279e+01; q[10][15]=3.8741359395934e+01; q[10][16]=6.6524559321657e+01; q[10][17]=1.7071378554833e+01; q[10][18]=2.3234516108847e+01; q[10][19]=4.8247261078055e+01; q[11][12]=4.8092094826036e+01; q[11][13]=3.3887559483420e+00; q[11][14]=2.6368577564199e+01; q[11][15]=5.5679895711418e+01; q[11][16]=7.1750284708933e+01; q[11][17]=1.2631893872825e+01; q[11][18]=2.6932728996777e+01; q[11][19]=1.0000000000000e+00; q[12][13]=4.7798798034572e+01; q[12][14]=9.9165053447429e+00; q[12][15]=5.8505442466161e+01; q[12][16]=2.7798190504760e+02; q[12][17]=1.1427000119701e+01; q[12][18]=2.1029990530586e+01; q[12][19]=2.0397078683768e+02; q[13][14]=9.1089574817139e+00; q[13][15]=3.3835737720574e+01; q[13][16]=1.7815549567056e+01; q[13][17]=4.1272404968214e+00; q[13][18]=2.4504156395152e+02; q[13][19]=3.3435675442163e+00; q[14][15]=8.9421193040709e+01; q[14][16]=6.7485067008375e+01; q[14][17]=2.2161693733113e+00; q[14][18]=8.5338209390745e+00; q[14][19]=4.3342126659660e+00; q[15][16]=3.1432036618746e+02; q[15][17]=2.0305343047059e+01; q[15][18]=3.4167877957799e+01; q[15][19]=1.0000000000000e+00; q[16][17]=5.2559565123081e+00; q[16][18]=2.0382362288681e+01; q[16][19]=1.0765527137500e+02; q[17][18]=1.3814733274637e+01; q[17][19]=2.8259139240676e+00; q[18][19]=1.0000000000000e+00; /* amino acid frequencies */ f[0]=0.072; f[1]=0.019; f[2]=0.039; f[3]=0.019; f[4]=0.006; f[5]=0.025; f[6]=0.024; f[7]=0.056; f[8]=0.028; f[9]=0.088; f[10]=0.168; f[11]=0.023; f[12]=0.054; f[13]=0.061; f[14]=0.054; f[15]=0.072; f[16]=0.086; f[17]=0.029; f[18]=0.033; f[19]=0.043; } /* mtrevdata */ void blosum62data(dmatrix q, double *f) { /* * BLOSUM62 model of amino acid evolution * * S. Henikoff and J. G. Henikoff. 1992. PNAS USA 89:10915-10919. * */ q[0][1]=7.3579038969751e-01; q[0][2]=4.8539105546575e-01; q[0][3]=5.4316182089867e-01; q[0][4]=1.4599953104700e+00; q[0][5]=1.1997057046020e+00; q[0][6]=1.1709490427999e+00; q[0][7]=1.9558835749595e+00; q[0][8]=7.1624144499779e-01; q[0][9]=6.0589900368677e-01; q[0][10]=8.0001653051838e-01; q[0][11]=1.2952012667833e+00; q[0][12]=1.2537582666635e+00; q[0][13]=4.9296467974759e-01; q[0][14]=1.1732759009239e+00; q[0][15]=4.3250926870566e+00; q[0][16]=1.7291780194850e+00; q[0][17]=4.6583936772479e-01; q[0][18]=7.1820669758623e-01; q[0][19]=2.1877745220045e+00; q[1][2]=1.2974467051337e+00; q[1][3]=5.0096440855513e-01; q[1][4]=2.2782657420895e-01; q[1][5]=3.0208336100636e+00; q[1][6]=1.3605741904203e+00; q[1][7]=4.1876330851753e-01; q[1][8]=1.4561411663360e+00; q[1][9]=2.3203644514174e-01; q[1][10]=6.2271166969249e-01; q[1][11]=5.4111151414889e+00; q[1][12]=9.8369298745695e-01; q[1][13]=3.7164469320875e-01; q[1][14]=4.4813366171831e-01; q[1][15]=1.1227831042096e+00; q[1][16]=9.1466595456337e-01; q[1][17]=4.2638231012175e-01; q[1][18]=7.2051744121611e-01; q[1][19]=4.3838834377202e-01; q[2][3]=3.1801000482161e+00; q[2][4]=3.9735894989702e-01; q[2][5]=1.8392161469920e+00; q[2][6]=1.2404885086396e+00; q[2][7]=1.3558723444845e+00; q[2][8]=2.4145014342081e+00; q[2][9]=2.8301732627800e-01; q[2][10]=2.1188815961519e-01; q[2][11]=1.5931370434574e+00; q[2][12]=6.4844127878707e-01; q[2][13]=3.5486124922252e-01; q[2][14]=4.9488704370192e-01; q[2][15]=2.9041016564560e+00; q[2][16]=1.8981736345332e+00; q[2][17]=1.9148204624678e-01; q[2][18]=5.3822251903674e-01; q[2][19]=3.1285879799342e-01; q[3][4]=2.4083661480204e-01; q[3][5]=1.1909457033960e+00; q[3][6]=3.7616252083685e+00; q[3][7]=7.9847324896839e-01; q[3][8]=7.7814266402188e-01; q[3][9]=4.1855573246161e-01; q[3][10]=2.1813157759360e-01; q[3][11]=1.0324479249521e+00; q[3][12]=2.2262189795786e-01; q[3][13]=2.8173069420651e-01; q[3][14]=7.3062827299842e-01; q[3][15]=1.5827541420653e+00; q[3][16]=9.3418750943056e-01; q[3][17]=1.4534504627853e-01; q[3][18]=2.6142220896504e-01; q[3][19]=2.5812928941763e-01; q[4][5]=3.2980150463028e-01; q[4][6]=1.4074889181440e-01; q[4][7]=4.1820319228376e-01; q[4][8]=3.5405810983129e-01; q[4][9]=7.7489402279418e-01; q[4][10]=8.3184264014158e-01; q[4][11]=2.8507880090648e-01; q[4][12]=7.6768882347954e-01; q[4][13]=4.4133747118660e-01; q[4][14]=3.5600849876863e-01; q[4][15]=1.1971884150942e+00; q[4][16]=1.1198313585160e+00; q[4][17]=5.2766441887169e-01; q[4][18]=4.7023773369610e-01; q[4][19]=1.1163524786062e+00; q[5][6]=5.5289191779282e+00; q[5][7]=6.0984630538281e-01; q[5][8]=2.4353411311401e+00; q[5][9]=2.3620245120365e-01; q[5][10]=5.8073709318144e-01; q[5][11]=3.9452776745146e+00; q[5][12]=2.4948960771127e+00; q[5][13]=1.4435695975031e-01; q[5][14]=8.5857057567418e-01; q[5][15]=1.9348709245965e+00; q[5][16]=1.2774802945956e+00; q[5][17]=7.5865380864172e-01; q[5][18]=9.5898974285014e-01; q[5][19]=5.3078579012486e-01; q[6][7]=4.2357999217628e-01; q[6][8]=1.6268910569817e+00; q[6][9]=1.8684804693170e-01; q[6][10]=3.7262517508685e-01; q[6][11]=2.8024271516787e+00; q[6][12]=5.5541539747043e-01; q[6][13]=2.9140908416530e-01; q[6][14]=9.2656393484598e-01; q[6][15]=1.7698932389373e+00; q[6][16]=1.0710972360073e+00; q[6][17]=4.0763564893830e-01; q[6][18]=5.9671930034577e-01; q[6][19]=5.2425384633796e-01; q[7][8]=5.3985912495418e-01; q[7][9]=1.8929629237636e-01; q[7][10]=2.1772115923623e-01; q[7][11]=7.5204244030271e-01; q[7][12]=4.5943617357855e-01; q[7][13]=3.6816646445253e-01; q[7][14]=5.0408659952683e-01; q[7][15]=1.5093262532236e+00; q[7][16]=6.4143601140497e-01; q[7][17]=5.0835892463812e-01; q[7][18]=3.0805573703500e-01; q[7][19]=2.5334079019018e-01; q[8][9]=2.5271844788492e-01; q[8][10]=3.4807220979697e-01; q[8][11]=1.0225070358890e+00; q[8][12]=9.8431152535870e-01; q[8][13]=7.1453370392764e-01; q[8][14]=5.2700733915060e-01; q[8][15]=1.1170297629105e+00; q[8][16]=5.8540709022472e-01; q[8][17]=3.0124860078016e-01; q[8][18]=4.2189539693890e+00; q[8][19]=2.0155597175031e-01; q[9][10]=3.8909637733035e+00; q[9][11]=4.0619358664202e-01; q[9][12]=3.3647977631042e+00; q[9][13]=1.5173593259539e+00; q[9][14]=3.8835540920564e-01; q[9][15]=3.5754441245967e-01; q[9][16]=1.1790911972601e+00; q[9][17]=3.4198578754023e-01; q[9][18]=6.7461709322842e-01; q[9][19]=8.3118394054582e+00; q[10][11]=4.4557027426059e-01; q[10][12]=6.0305593795716e+00; q[10][13]=2.0648397032375e+00; q[10][14]=3.7455568747097e-01; q[10][15]=3.5296918452729e-01; q[10][16]=9.1525985769421e-01; q[10][17]=6.9147463459998e-01; q[10][18]=8.1124585632307e-01; q[10][19]=2.2314056889131e+00; q[11][12]=1.0730611843319e+00; q[11][13]=2.6692475051102e-01; q[11][14]=1.0473834507215e+00; q[11][15]=1.7521659178195e+00; q[11][16]=1.3038752007987e+00; q[11][17]=3.3224304063396e-01; q[11][18]=7.1799348690032e-01; q[11][19]=4.9813847530407e-01; q[12][13]=1.7738551688305e+00; q[12][14]=4.5412362510273e-01; q[12][15]=9.1872341574605e-01; q[12][16]=1.4885480537218e+00; q[12][17]=8.8810109815193e-01; q[12][18]=9.5168216224591e-01; q[12][19]=2.5758507553153e+00; q[13][14]=2.3359790962888e-01; q[13][15]=5.4002764482413e-01; q[13][16]=4.8820611879305e-01; q[13][17]=2.0743248934965e+00; q[13][18]=6.7472604308008e+00; q[13][19]=8.3811961017754e-01; q[14][15]=1.1691295777157e+00; q[14][16]=1.0054516831488e+00; q[14][17]=2.5221483002727e-01; q[14][18]=3.6940531935451e-01; q[14][19]=4.9690841067567e-01; q[15][16]=5.1515562922704e+00; q[15][17]=3.8792562209837e-01; q[15][18]=7.9675152076106e-01; q[15][19]=5.6192545744165e-01; q[16][17]=5.1312812689059e-01; q[16][18]=8.0101024319939e-01; q[16][19]=2.2530740511763e+00; q[17][18]=4.0544190065580e+00; q[17][19]=2.6650873142646e-01; q[18][19]=1.0000000000000e+00; f[0]=0.074; f[1]=0.052; f[2]=0.045; f[3]=0.054; f[4]=0.025; f[5]=0.034; f[6]=0.054; f[7]=0.074; f[8]=0.026; f[9]=0.068; f[10]=0.099; f[11]=0.058; f[12]=0.025; f[13]=0.047; f[14]=0.039; f[15]=0.057; f[16]=0.051; f[17]=0.013; f[18]=0.032; f[19]=0.073; } /* blosum62data */ void vtmvdata(dmatrix q, double *f) { /* * Dayhoff model for amino acid evolution * Mueller, T. and Vingron, M. * "Modeling Amino Acid Replacement" * Journal of Comp. Biology, 7(6):761-776,2000 */ /* amino acid frequencies */ f[ 0]=0.0770764620135024 ; f[ 1]=0.0500819370772208 ; f[ 2]=0.0462377395993731 ; f[ 3]=0.0537929860758246 ; f[ 4]=0.0144533387583345 ; f[ 5]=0.0408923608974345 ; f[ 6]=0.0633579339160905 ; f[ 7]=0.0655672355884439 ; f[ 8]=0.0218802687005936 ; f[ 9]=0.0591969699027449 ; f[10]=0.0976461276528445 ; f[11]=0.0592079410822730 ; f[12]=0.0220695876653368 ; f[13]=0.0413508521834260 ; f[14]=0.0476871596856874 ; f[15]=0.0707295165111524 ; f[16]=0.0567759161524817 ; f[17]=0.0127019797647213 ; f[18]=0.0323746050281867 ; f[19]=0.0669190817443274 ; /* relative rates */ q[ 0][ 1] = 1.2412691067876198; q[ 0][ 2] = 1.2184237953498958; q[ 0][ 3] = 1.3759368509441177; q[ 0][ 4] = 2.4731223087544874; q[ 0][ 5] = 2.2155167805137470; q[ 0][ 6] = 2.3379911207495061; q[ 0][ 7] = 3.3386555146457697; q[ 0][ 8] = 0.9615841926910841; q[ 0][ 9] = 0.8908203061925510; q[ 0][10] = 1.0778497408764076; q[ 0][11] = 1.4932055816372476; q[ 0][12] = 1.9006455961717605; q[ 0][13] = 0.6883439026872615; q[ 0][14] = 2.7355620089953550; q[ 0][15] = 6.4208961859142883; q[ 0][16] = 5.2892514169776437; q[ 0][17] = 0.5488578478106930; q[ 0][18] = 0.5411769916657778; q[ 0][19] = 4.6501894691803214; q[ 1][ 2] = 1.5720770753326880; q[ 1][ 3] = 0.7550654439001206; q[ 1][ 4] = 1.4414262567428417; q[ 1][ 5] = 5.5120819705248678; q[ 1][ 6] = 1.3542404860613146; q[ 1][ 7] = 1.3121700301622004; q[ 1][ 8] = 4.9238668283945266; q[ 1][ 9] = 0.4323005487925516; q[ 1][10] = 0.8386701149158265; q[ 1][11] = 10.0173308173660018; q[ 1][12] = 1.2488638689609959; q[ 1][13] = 0.4224945197276290; q[ 1][14] = 1.3091837782420783; q[ 1][15] = 1.9202994262316166; q[ 1][16] = 1.3363401740560601; q[ 1][17] = 1.5170142153962840; q[ 1][18] = 0.8912614404565405; q[ 1][19] = 0.7807017855806767; q[ 2][ 3] = 7.8584219153689405; q[ 2][ 4] = 0.9784679122774127; q[ 2][ 5] = 3.0143201670924822; q[ 2][ 6] = 2.0093434778398112; q[ 2][ 7] = 2.4117632898861809; q[ 2][ 8] = 6.1974384977884114; q[ 2][ 9] = 0.9179291175331520; q[ 2][10] = 0.4098311270816011; q[ 2][11] = 4.4034547578962568; q[ 2][12] = 0.9378803706165143; q[ 2][13] = 0.5044944273324311; q[ 2][14] = 0.7103720531974738; q[ 2][15] = 6.1234512396801764; q[ 2][16] = 3.8852506105922231; q[ 2][17] = 0.1808525752605976; q[ 2][18] = 1.0894926581511342; q[ 2][19] = 0.4586061981719967; q[ 3][ 4] = 0.2272488448121475; q[ 3][ 5] = 1.6562495638176040; q[ 3][ 6] = 9.6883451875685065; q[ 3][ 7] = 1.9142079025990228; q[ 3][ 8] = 2.1459640610133781; q[ 3][ 9] = 0.2161660372725585; q[ 3][10] = 0.3574207468998517; q[ 3][11] = 1.4521790561663968; q[ 3][12] = 0.4075239926000898; q[ 3][13] = 0.1675129724559251; q[ 3][14] = 1.0714605979577547; q[ 3][15] = 2.2161944596741829; q[ 3][16] = 1.5066839872944762; q[ 3][17] = 0.2496584188151770; q[ 3][18] = 0.7447620891784513; q[ 3][19] = 0.4594535241660911; q[ 4][ 5] = 0.4587469126746136; q[ 4][ 6] = 0.4519167943192672; q[ 4][ 7] = 1.1034605684472507; q[ 4][ 8] = 1.5196756759380692; q[ 4][ 9] = 0.9126668032539315; q[ 4][10] = 1.4081315998413697; q[ 4][11] = 0.3371091785647479; q[ 4][12] = 1.2213054800811556; q[ 4][13] = 1.6953951980808002; q[ 4][14] = 0.4326227078645523; q[ 4][15] = 3.6366815408744255; q[ 4][16] = 1.7557065205837685; q[ 4][17] = 1.6275179891253113; q[ 4][18] = 2.1579775140421025; q[ 4][19] = 2.2627456996290891; q[ 5][ 6] = 6.8124601839937675; q[ 5][ 7] = 0.8776110594765502; q[ 5][ 8] = 7.9943228564946525; q[ 5][ 9] = 0.4882733432879921; q[ 5][10] = 1.3318097154194044; q[ 5][11] = 6.0519085243118811; q[ 5][12] = 1.9106190827629084; q[ 5][13] = 0.3573432522499545; q[ 5][14] = 2.3019177728300728; q[ 5][15] = 2.3193703643237220; q[ 5][16] = 2.1576510103471440; q[ 5][17] = 0.8959082681546182; q[ 5][18] = 0.9183596801412757; q[ 5][19] = 0.6366932501396869; q[ 6][ 7] = 1.3860121390169038; q[ 6][ 8] = 1.6360079688522375; q[ 6][ 9] = 0.4035497929633328; q[ 6][10] = 0.5610717242294755; q[ 6][11] = 4.3290086529582830; q[ 6][12] = 0.7471936218068498; q[ 6][13] = 0.2317194387691585; q[ 6][14] = 1.5132807416252063; q[ 6][15] = 1.8273535587773553; q[ 6][16] = 1.5839981708584689; q[ 6][17] = 0.4198391148111098; q[ 6][18] = 0.5818111331782764; q[ 6][19] = 0.8940572875547330; q[ 7][ 8] = 0.8561248973045037; q[ 7][ 9] = 0.2888075033037488; q[ 7][10] = 0.3578662395745526; q[ 7][11] = 0.8945563662345198; q[ 7][12] = 0.5954812791740037; q[ 7][13] = 0.3693722640980460; q[ 7][14] = 0.7744933618134962; q[ 7][15] = 3.0637776193717610; q[ 7][16] = 0.7147489676267383; q[ 7][17] = 0.9349753595598769; q[ 7][18] = 0.3374467649724478; q[ 7][19] = 0.6193321034173915; q[ 8][ 9] = 0.5787937115407940; q[ 8][10] = 1.0765007949562073; q[ 8][11] = 1.8085136096039203; q[ 8][12] = 1.3808291710019667; q[ 8][13] = 1.3629765501081097; q[ 8][14] = 1.8370555852070649; q[ 8][15] = 1.9699895187387506; q[ 8][16] = 1.6136654573285647; q[ 8][17] = 0.6301954684360302; q[ 8][18] = 7.7587442309146040; q[ 8][19] = 0.5333220944030346; q[ 9][10] = 6.0019110258426362; q[ 9][11] = 0.6244297525127139; q[ 9][12] = 6.7597899772045418; q[ 9][13] = 2.2864286949316077; q[ 9][14] = 0.4811402387911145; q[ 9][15] = 0.6047491507504744; q[ 9][16] = 2.6344778384442731; q[ 9][17] = 0.5604648274060783; q[ 9][18] = 0.8626796044156272; q[ 9][19] = 14.8729334615190609; q[10][11] = 0.5642322882556321; q[10][12] = 8.0327792947421148; q[10][13] = 4.3611548063555778; q[10][14] = 1.0084320519837335; q[10][15] = 0.8953754669269811; q[10][16] = 1.0192004372506540; q[10][17] = 1.5183114434679339; q[10][18] = 1.2452243224541324; q[10][19] = 3.5458093276667237; q[11][12] = 1.7129670976916258; q[11][13] = 0.3910559903834828; q[11][14] = 1.3918935593582853; q[11][15] = 1.9776630140912268; q[11][16] = 2.5513781312660280; q[11][17] = 0.5851920879490173; q[11][18] = 0.7835447533710449; q[11][19] = 0.7801080335991272; q[12][13] = 2.3201373546296349; q[12][14] = 0.4953193808676289; q[12][15] = 1.0657482318076852; q[12][16] = 3.3628488360462363; q[12][17] = 1.4680478689711018; q[12][18] = 1.0899165770956820; q[12][19] = 4.0584577156753401; q[13][14] = 0.3746821107962129; q[13][15] = 1.1079144700606407; q[13][16] = 0.6882725908872254; q[13][17] = 3.3448437239772266; q[13][18] = 10.3848523331334590; q[13][19] = 1.7039730522675411; q[14][15] = 3.5465914843628927; q[14][16] = 1.9485376673137556; q[14][17] = 0.4326058001438786; q[14][18] = 0.4819109019647465; q[14][19] = 0.5985498912985666; q[15][16] = 8.8479984061248178; q[15][17] = 0.6791126595939816; q[15][18] = 0.9547229305958682; q[15][19] = 0.9305232113028208; q[16][17] = 0.4514203099376473; q[16][18] = 0.8564314184691215; q[16][19] = 3.4242218450865543; q[17][18] = 4.5377235790405388; q[17][19] = 0.5658969249032649; q[18][19] = 1.0000000000000000; } /* vtmvdata */ /* * WAG matrix: Simon Whelan and Nick Goldman * */ void wagdata(dmatrix q, double *f) { /* * WAG model of amino acid evolution * * Whelan, S. and N. Goldman (2001) * A general empirical model of protein evolution * derived from multiple protein families using a * maximum likelihood approach. * Mol. Biol. Evol. 18:691-699 * */ /* R matrix */ q[0][1] =0.551571; q[0][2] =0.509848; q[1][2] =0.635346; q[0][3] =0.738998; q[1][3] =0.147304; q[2][3] =5.429420; q[0][4] =1.027040; q[1][4] =0.528191; q[2][4] =0.265256; q[3][4] =0.0302949; q[0][5] =0.908598; q[1][5] =3.035500; q[2][5] =1.543640; q[3][5] =0.616783; q[4][5] =0.0988179; q[0][6] =1.582850; q[1][6] =0.439157; q[2][6] =0.947198; q[3][6] =6.174160; q[4][6] =0.021352; q[5][6] =5.469470; q[0][7] =1.416720; q[1][7] =0.584665; q[2][7] =1.125560; q[3][7] =0.865584; q[4][7] =0.306674; q[5][7] =0.330052; q[6][7] =0.567717; q[0][8] =0.316954; q[1][8] =2.137150; q[2][8] =3.956290; q[3][8] =0.930676; q[4][8] =0.248972; q[5][8] =4.294110; q[6][8] =0.570025; q[7][8] =0.249410; q[0][9] =0.193335; q[1][9] =0.186979; q[2][9] =0.554236; q[3][9] =0.039437; q[4][9] =0.170135; q[5][9] =0.113917; q[6][9] =0.127395; q[7][9] =0.0304501; q[8][9] =0.138190; q[0][10] =0.397915; q[1][10] =0.497671; q[2][10] =0.131528; q[3][10] =0.0848047; q[4][10] =0.384287; q[5][10] =0.869489; q[6][10] =0.154263; q[7][10] =0.0613037; q[8][10] =0.499462; q[9][10] =3.170970; q[0][11] =0.906265; q[1][11] =5.351420; q[2][11] =3.012010; q[3][11] =0.479855; q[4][11] =0.0740339; q[5][11] =3.894900; q[6][11] =2.584430; q[7][11] =0.373558; q[8][11] =0.890432; q[9][11] =0.323832; q[10][11]=0.257555; q[0][12] =0.893496; q[1][12] =0.683162; q[2][12] =0.198221; q[3][12] =0.103754; q[4][12] =0.390482; q[5][12] =1.545260; q[6][12] =0.315124; q[7][12] =0.174100; q[8][12] =0.404141; q[9][12] =4.257460; q[10][12]=4.854020; q[11][12]=0.934276; q[0][13] =0.210494; q[1][13] =0.102711; q[2][13] =0.0961621; q[3][13] =0.0467304; q[4][13] =0.398020; q[5][13] =0.0999208; q[6][13] =0.0811339; q[7][13] =0.049931; q[8][13] =0.679371; q[9][13] =1.059470; q[10][13]=2.115170; q[11][13]=0.088836; q[12][13]=1.190630; q[0][14] =1.438550; q[1][14] =0.679489; q[2][14] =0.195081; q[3][14] =0.423984; q[4][14] =0.109404; q[5][14] =0.933372; q[6][14] =0.682355; q[7][14] =0.243570; q[8][14] =0.696198; q[9][14] =0.0999288; q[10][14]=0.415844; q[11][14]=0.556896; q[12][14]=0.171329; q[13][14]=0.161444; q[0][15] =3.370790; q[1][15] =1.224190; q[2][15] =3.974230; q[3][15] =1.071760; q[4][15] =1.407660; q[5][15] =1.028870; q[6][15] =0.704939; q[7][15] =1.341820; q[8][15] =0.740169; q[9][15] =0.319440; q[10][15]=0.344739; q[11][15]=0.967130; q[12][15]=0.493905; q[13][15]=0.545931; q[14][15]=1.613280; q[0][16] =2.121110; q[1][16] =0.554413; q[2][16] =2.030060; q[3][16] =0.374866; q[4][16] =0.512984; q[5][16] =0.857928; q[6][16] =0.822765; q[7][16] =0.225833; q[8][16] =0.473307; q[9][16] =1.458160; q[10][16]=0.326622; q[11][16]=1.386980; q[12][16]=1.516120; q[13][16]=0.171903; q[14][16]=0.795384; q[15][16]=4.378020; q[0][17] =0.113133; q[1][17] =1.163920; q[2][17] =0.0719167; q[3][17] =0.129767; q[4][17] =0.717070; q[5][17] =0.215737; q[6][17] =0.156557; q[7][17] =0.336983; q[8][17] =0.262569; q[9][17] =0.212483; q[10][17]=0.665309; q[11][17]=0.137505; q[12][17]=0.515706; q[13][17]=1.529640; q[14][17]=0.139405; q[15][17]=0.523742; q[16][17]=0.110864; q[0][18] =0.240735; q[1][18] =0.381533; q[2][18] =1.086000; q[3][18] =0.325711; q[4][18] =0.543833; q[5][18] =0.227710; q[6][18] =0.196303; q[7][18] =0.103604; q[8][18] =3.873440; q[9][18] =0.420170; q[10][18]=0.398618; q[11][18]=0.133264; q[12][18]=0.428437; q[13][18]=6.454280; q[14][18]=0.216046; q[15][18]=0.786993; q[16][18]=0.291148; q[17][18]=2.485390; q[0][19] =2.006010; q[1][19] =0.251849; q[2][19] =0.196246; q[3][19] =0.152335; q[4][19] =1.002140; q[5][19] =0.301281; q[6][19] =0.588731; q[7][19] =0.187247; q[8][19] =0.118358; q[9][19] =7.821300; q[10][19]=1.800340; q[11][19]=0.305434; q[12][19]=2.058450; q[13][19]=0.649892; q[14][19]=0.314887; q[15][19]=0.232739; q[16][19]=1.388230; q[17][19]=0.365369; q[18][19]=0.314730; f[ 0] = 0.0866279; f[ 1] = 0.043972; f[ 2] = 0.0390894; f[ 3] = 0.0570451; f[ 4] = 0.0193078; f[ 5] = 0.0367281; f[ 6] = 0.0580589; f[ 7] = 0.0832518; f[ 8] = 0.0244313; f[ 9] = 0.048466; f[10] = 0.086209; f[11] = 0.0620286; f[12] = 0.0195027; f[13] = 0.0384319; f[14] = 0.0457631; f[15] = 0.0695179; f[16] = 0.0610127; f[17] = 0.0143859; f[18] = 0.0352742; f[19] = 0.0708956; } /* wagdata */ /* * old WAG matrix: Simon Whelan and Nick Goldman * */ void oldwagdata(dmatrix q, double *f) { /* * WAG model of amino acid evolution * * S. Whelan and N. Goldman. 2000. In prep. * * presented at the MASAMB-X workshop in Cambridge * * Whelan, S., and N. Goldman. 2000. * The WAG amino acid rate matrix. * Manuscript in prep. * * old version - differed from the published matrix */ /* Q matrix */ q[0][1] = 0.610810; q[0][2] = 0.569079; q[0][3] = 0.821500; q[0][4] = 1.141050; q[0][5] = 1.011980; q[0][6] = 1.756410; q[0][7] = 1.572160; q[0][8] = 0.354813; q[0][9] = 0.219023; q[0][10] = 0.443935; q[0][11] = 1.005440; q[0][12] = 0.989475; q[0][13] = 0.233492; q[0][14] = 1.594890; q[0][15] = 3.733380; q[0][16] = 2.349220; q[0][17] = 0.125227; q[0][18] = 0.268987; q[0][19] = 2.221870; q[1][2] = 0.711690; q[1][3] = 0.165074; q[1][4] = 0.585809; q[1][5] = 3.360330; q[1][6] = 0.488649; q[1][7] = 0.650469; q[1][8] = 2.362040; q[1][9] = 0.206722; q[1][10] = 0.551450; q[1][11] = 5.925170; q[1][12] = 0.758446; q[1][13] = 0.116821; q[1][14] = 0.753467; q[1][15] = 1.357640; q[1][16] = 0.613776; q[1][17] = 1.294610; q[1][18] = 0.423612; q[1][19] = 0.280336; q[2][3] = 6.013660; q[2][4] = 0.296524; q[2][5] = 1.716740; q[2][6] = 1.056790; q[2][7] = 1.253910; q[2][8] = 4.378930; q[2][9] = 0.615636; q[2][10] = 0.147156; q[2][11] = 3.334390; q[2][12] = 0.224747; q[2][13] = 0.110793; q[2][14] = 0.217538; q[2][15] = 4.394450; q[2][16] = 2.257930; q[2][17] = 0.078463; q[2][18] = 1.208560; q[2][19] = 0.221176; q[3][4] = 0.033379; q[3][5] = 0.691268; q[3][6] = 6.833400; q[3][7] = 0.961142; q[3][8] = 1.032910; q[3][9] = 0.043523; q[3][10] = 0.093930; q[3][11] = 0.533362; q[3][12] = 0.116813; q[3][13] = 0.052004; q[3][14] = 0.472601; q[3][15] = 1.192810; q[3][16] = 0.417372; q[3][17] = 0.146348; q[3][18] = 0.363243; q[3][19] = 0.169417; q[4][5] = 0.109261; q[4][6] = 0.023920; q[4][7] = 0.341086; q[4][8] = 0.275403; q[4][9] = 0.189890; q[4][10] = 0.428414; q[4][11] = 0.083649; q[4][12] = 0.437393; q[4][13] = 0.441300; q[4][14] = 0.122303; q[4][15] = 1.560590; q[4][16] = 0.570186; q[4][17] = 0.795736; q[4][18] = 0.604634; q[4][19] = 1.114570; q[5][6] = 6.048790; q[5][7] = 0.366510; q[5][8] = 4.749460; q[5][9] = 0.131046; q[5][10] = 0.964886; q[5][11] = 4.308310; q[5][12] = 1.705070; q[5][13] = 0.110744; q[5][14] = 1.036370; q[5][15] = 1.141210; q[5][16] = 0.954144; q[5][17] = 0.243615; q[5][18] = 0.252457; q[5][19] = 0.333890; q[6][7] = 0.630832; q[6][8] = 0.635025; q[6][9] = 0.141320; q[6][10] = 0.172579; q[6][11] = 2.867580; q[6][12] = 0.353912; q[6][13] = 0.092310; q[6][14] = 0.755791; q[6][15] = 0.782467; q[6][16] = 0.914814; q[6][17] = 0.172682; q[6][18] = 0.217549; q[6][19] = 0.655045; q[7][8] = 0.276379; q[7][9] = 0.034151; q[7][10] = 0.068651; q[7][11] = 0.415992; q[7][12] = 0.194220; q[7][13] = 0.055288; q[7][14] = 0.273149; q[7][15] = 1.486700; q[7][16] = 0.251477; q[7][17] = 0.374321; q[7][18] = 0.114187; q[7][19] = 0.209108; q[8][9] = 0.152215; q[8][10] = 0.555096; q[8][11] = 0.992083; q[8][12] = 0.450867; q[8][13] = 0.756080; q[8][14] = 0.771387; q[8][15] = 0.822459; q[8][16] = 0.525511; q[8][17] = 0.289998; q[8][18] = 4.290350; q[8][19] = 0.131869; q[9][10] = 3.517820; q[9][11] = 0.360574; q[9][12] = 4.714220; q[9][13] = 1.177640; q[9][14] = 0.111502; q[9][15] = 0.353443; q[9][16] = 1.615050; q[9][17] = 0.234326; q[9][18] = 0.468951; q[9][19] = 8.659740; q[10][11] = 0.287583; q[10][12] = 5.375250; q[10][13] = 2.348200; q[10][14] = 0.462018; q[10][15] = 0.382421; q[10][16] = 0.364222; q[10][17] = 0.740259; q[10][18] = 0.443205; q[10][19] = 1.997370; q[11][12] = 1.032220; q[11][13] = 0.098843; q[11][14] = 0.619503; q[11][15] = 1.073780; q[11][16] = 1.537920; q[11][17] = 0.152232; q[11][18] = 0.147411; q[11][19] = 0.342012; q[12][13] = 1.320870; q[12][14] = 0.194864; q[12][15] = 0.556353; q[12][16] = 1.681970; q[12][17] = 0.570369; q[12][18] = 0.473810; q[12][19] = 2.282020; q[13][14] = 0.179896; q[13][15] = 0.606814; q[13][16] = 0.191467; q[13][17] = 1.699780; q[13][18] = 7.154480; q[13][19] = 0.725096; q[14][15] = 1.786490; q[14][16] = 0.885349; q[14][17] = 0.156619; q[14][18] = 0.239607; q[14][19] = 0.351250; q[15][16] = 4.847130; q[15][17] = 0.578784; q[15][18] = 0.872519; q[15][19] = 0.258861; q[16][17] = 0.126678; q[16][18] = 0.325490; q[16][19] = 1.547670; q[17][18] = 2.763540; q[17][19] = 0.409817; q[18][19] = 0.347826; /* original frequencies */ f[ 0] = 0.0866; f[ 1] = 0.0440; f[ 2] = 0.0391; f[ 3] = 0.0570; f[ 4] = 0.0193; f[ 5] = 0.0367; f[ 6] = 0.0581; f[ 7] = 0.0833; f[ 8] = 0.0244; f[ 9] = 0.0485; f[10] = 0.0862; f[11] = 0.0620; f[12] = 0.0195; f[13] = 0.0384; f[14] = 0.0458; f[15] = 0.0695; f[16] = 0.0610; f[17] = 0.0144; f[18] = 0.0353; f[19] = 0.0709; } /* oldwagdata */ void cprev45data(dmatrix q, double *f) { /* cpREV45 model of amino acid evolution * Adachi, J., P.J. Waddell, W. Martin, and M. Hasegawa. 2000. * J. Mol. Evol. 50:348-358 * (reconstructed from 45 chloroplast genomes) */ q[0][1] = 105; q[0][2] = 227; q[0][3] = 175; q[0][4] = 669; q[0][5] = 157; q[0][6] = 499; q[0][7] = 665; q[0][8] = 66; q[0][9] = 145; q[0][10] = 197; q[0][11] = 236; q[0][12] = 185; q[0][13] = 68; q[0][14] = 490; q[0][15] = 2440; q[0][16] = 1340; q[0][17] = 14; q[0][18] = 56; q[0][19] = 968; q[1][2] = 357; q[1][3] = 43; q[1][4] = 823; q[1][5] = 1745; q[1][6] = 152; q[1][7] = 243; q[1][8] = 715; q[1][9] = 136; q[1][10] = 203; q[1][11] = 4482; q[1][12] = 125; q[1][13] = 53; q[1][14] = 87; q[1][15] = 385; q[1][16] = 314; q[1][17] = 230; q[1][18] = 323; q[1][19] = 92; q[2][3] = 4435; q[2][4] = 538; q[2][5] = 768; q[2][6] = 1055; q[2][7] = 653; q[2][8] = 1405; q[2][9] = 168; q[2][10] = 113; q[2][11] = 2430; q[2][12] = 61; q[2][13] = 97; q[2][14] = 173; q[2][15] = 2085; q[2][16] = 1393; q[2][17] = 40; q[2][18] = 754; q[2][19] = 83; q[3][4] = 10; q[3][5] = 400; q[3][6] = 3691; q[3][7] = 431; q[3][8] = 331; q[3][9] = 10; q[3][10] = 10; q[3][11] = 412; q[3][12] = 47; q[3][13] = 22; q[3][14] = 170; q[3][15] = 590; q[3][16] = 266; q[3][17] = 18; q[3][18] = 281; q[3][19] = 75; q[4][5] = 10; q[4][6] = 10; q[4][7] = 303; q[4][8] = 441; q[4][9] = 280; q[4][10] = 396; q[4][11] = 48; q[4][12] = 159; q[4][13] = 726; q[4][14] = 285; q[4][15] = 2331; q[4][16] = 576; q[4][17] = 435; q[4][18] = 1466; q[4][19] = 592; q[5][6] = 3122; q[5][7] = 133; q[5][8] = 1269; q[5][9] = 92; q[5][10] = 286; q[5][11] = 3313; q[5][12] = 202; q[5][13] = 10; q[5][14] = 323; q[5][15] = 396; q[5][16] = 241; q[5][17] = 53; q[5][18] = 391; q[5][19] = 54; q[6][7] = 379; q[6][8] = 162; q[6][9] = 148; q[6][10] = 82; q[6][11] = 2629; q[6][12] = 113; q[6][13] = 145; q[6][14] = 185; q[6][15] = 568; q[6][16] = 369; q[6][17] = 63; q[6][18] = 142; q[6][19] = 200; q[7][8] = 19; q[7][9] = 40; q[7][10] = 20; q[7][11] = 263; q[7][12] = 21; q[7][13] = 25; q[7][14] = 28; q[7][15] = 691; q[7][16] = 92; q[7][17] = 82; q[7][18] = 10; q[7][19] = 91; q[8][9] = 29; q[8][10] = 66; q[8][11] = 305; q[8][12] = 10; q[8][13] = 127; q[8][14] = 152; q[8][15] = 303; q[8][16] = 32; q[8][17] = 69; q[8][18] = 1971; q[8][19] = 25; q[9][10] = 1745; q[9][11] = 345; q[9][12] = 1772; q[9][13] = 454; q[9][14] = 117; q[9][15] = 216; q[9][16] = 1040; q[9][17] = 42; q[9][18] = 89; q[9][19] = 4797; q[10][11] = 218; q[10][12] = 1351; q[10][13] = 1268; q[10][14] = 219; q[10][15] = 516; q[10][16] = 156; q[10][17] = 159; q[10][18] = 189; q[10][19] = 865; q[11][12] = 193; q[11][13] = 72; q[11][14] = 302; q[11][15] = 868; q[11][16] = 918; q[11][17] = 10; q[11][18] = 247; q[11][19] = 249; q[12][13] = 327; q[12][14] = 100; q[12][15] = 93; q[12][16] = 645; q[12][17] = 86; q[12][18] = 215; q[12][19] = 475; q[13][14] = 43; q[13][15] = 487; q[13][16] = 148; q[13][17] = 468; q[13][18] = 2370; q[13][19] = 317; q[14][15] = 1202; q[14][16] = 260; q[14][17] = 49; q[14][18] = 97; q[14][19] = 122; q[15][16] = 2151; q[15][17] = 73; q[15][18] = 522; q[15][19] = 167; q[16][17] = 29; q[16][18] = 71; q[16][19] = 760; q[17][18] = 346; q[17][19] = 10; q[18][19] = 119; f[0] = 0.076; f[1] = 0.062; f[2] = 0.041; f[3] = 0.037; f[4] = 0.009; f[5] = 0.038; f[6] = 0.049; f[7] = 0.084; f[8] = 0.025; f[9] = 0.081; f[10] = 0.101; f[11] = 0.050; f[12] = 0.022; f[13] = 0.051; f[14] = 0.043; f[15] = 0.062; f[16] = 0.054; f[17] = 0.018; f[18] = 0.031; f[19] = 0.066; } /* cprev45data */ tree-puzzle-5.2/src/mlparam.c0000644000076400001440000003132510073365303011717 /* * mlparam.c * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifdef HAVE_CONFIG_H # include #endif #define EXTERN extern /* prototypes */ #include #include #include #include "puzzle.h" #include "util.h" #include "ml.h" #include "gamma.h" /******************************************************************************/ /* discrete Gamma-distribution and related stuff */ /******************************************************************************/ /* compare general base frequencies with frequencies of taxon i with chi square */ double homogentest(int taxon) { return chi2test(Freqtpm, Basecomp[taxon], gettpmradix(), &chi2fail); } /* discrete Gamma according to Yang 1994 (JME 39:306-314) */ void YangDiscreteGamma (double shape, int c, dvector x) { double twoc, mu; int i; twoc = 2.0*c; mu = 0.0; for (i = 0; i < c; i++) { /* corresponding rates */ x[i] = icdfGamma ( (2.0*i+1.0)/twoc, shape); mu += x[i]; } mu = mu/c; /* rescale for avarage rate of 1.0 */ for (i = 0; i < c; i++) { x[i] /= mu; } } /* compute rates of each category when rates are Gamma-distributed */ void updaterates() { int i; double alpha; if (numcats == 1) { Rates[0] = 1.0; return; } if (Geta == 0.0) { for (i = 0; i < numcats; i++) Rates[i] = 1.0; return; } alpha = (1.0 - Geta)/Geta; YangDiscreteGamma (alpha, numcats, Rates); /* if invariable sites are present */ for (i = 0; i < numcats; i++) Rates[i] = Rates[i]/(1.0-fracinv); /* check for very small rates */ for (i = 0; i < numcats; i++) if (Rates[i] < 0.000001) Rates[i] = 0.000001; } /******************************************************************************/ /* parameter estimation */ /******************************************************************************/ /* compute sample mean and standard deviation of sample mean */ void computestat(double *data, int n, double *mean, double *err) { int i; double sum; double temp; double avg; /* compute sample mean */ sum = 0; for (i = 0; i < n; i++) sum += data[i]; avg = sum/(double) n; (*mean) = avg; /* compute std. error of sample mean with curvature method */ sum = 0; for (i = 0; i < n; i++) { temp = data[i] - avg; sum += temp*temp; } if (n != 1) (*err) = sqrt(sum)/sqrt((double)(n-1)*n); /* unbiased estimator */ else (*err) = 0.0; /* if n == 1 */ } /* compute ML value of quartet (a,b,c,d) for parameter estimation with quartet subsampling */ double quartetml(int a, int b, int c, int d) { double d1, d2, d3; /* compute ML for all topologies */ if (approxp_optn) { /* approximate parameter mode */ d1 = quartet_alklhd(a,b,c,d); /* (a,b)-(c,d) */ d2 = quartet_alklhd(a,c,b,d); /* (a,c)-(b,d) */ d3 = quartet_alklhd(a,d,b,c); /* (a,d)-(b,c) */ } else { d1 = quartet_lklhd(a,b,c,d); /* (a,b)-(c,d) */ d2 = quartet_lklhd(a,c,b,d); /* (a,c)-(b,d) */ d3 = quartet_lklhd(a,d,b,c); /* (a,d)-(b,c) */ } /* looking for max(d1, d2, d3) */ if (d1 < d2) { /* d2 > d1 */ if (d2 < d3) { /* d3 > d2 > d1 */ /* d3 maximum */ return d3; } else { /* d2 >= d3 > d1 */ /* d2 maximum */ return d2; } } else { /* d1 >= d2 */ if (d1 < d3) { /* d3 > d1 >= d2 */ /* d3 maximum */ return d3; } else { /* d1 >= d2 && d1 >= d3 */ /* d1 maximum */ return d1; } } } /* optimization function TSparam - quartets */ double opttsq(double x) { if (x < MINTS) TSparam = MINTS; else if (x > MAXTS) TSparam = MAXTS; else TSparam = x; tranprobmat(); distupdate(qca, qcb, qcc, qcd); return (-quartetml(qca, qcb, qcc, qcd)); } /* optimization function YRparam - quartets */ double optyrq(double x) { if (x < MINYR) YRparam = MINYR; else if (x > MAXYR) YRparam = MAXYR; else YRparam = x; tranprobmat(); distupdate(qca, qcb, qcc, qcd); return (-quartetml(qca, qcb, qcc, qcd)); } /* estimate substitution process parameters - random quartets */ void optimseqevolparamsquart() { double tsmeanold, yrmeanold; dvector tslist, yrlist; int fin; ivector taxon; uli minqts, maxqts, n; taxon = new_ivector(4); /* number of quartets to be investigated */ minqts = (uli) floor(0.25 * MINPERTAXUM * Maxspc) + 1; maxqts = (uli) floor(0.25 * MAXPERTAXUM * Maxspc) + 1; if (Maxspc == 4) { minqts = (uli) 1; maxqts = (uli) 1; } tslist = new_dvector(maxqts); yrlist = new_dvector(maxqts); /* initialize averages */ tsmean = TSparam; yrmean = YRparam; fin = FALSE; /* investigate maxqts random quartets */ for (n = 0; n < maxqts; n++) { /* choose random quartet */ chooser(Maxspc, 4, taxon); /* * optimize parameters on this quartet */ qca = taxon[0]; qcb = taxon[1]; qcc = taxon[2]; qcd = taxon[3]; /* initialize start values with average value */ if ((SH_optn || nuc_optn) && optim_optn && (data_optn == 0)) TSparam = tsmean; if ((nuc_optn && TN_optn) && optim_optn && (data_optn == 0)) YRparam = yrmean; /* estimation */ twodimenmin(EPSILON_SUBSTPARAM, (SH_optn || nuc_optn) && optim_optn && (data_optn == 0), MINTS, &TSparam, MAXTS, opttsq, &tserr, (nuc_optn && TN_optn) && optim_optn && (data_optn == 0), MINYR, &YRparam, MAXYR, optyrq, &yrerr); tsmeanold = tsmean; yrmeanold = yrmean; tslist[n] = TSparam; yrlist[n] = YRparam; computestat(tslist, n+1 , &tsmean, &tserr); computestat(yrlist, n+1 , &yrmean, &yrerr); /* check whether the means are converging */ if (n > minqts-2) { if ((fabs(tsmean-tsmeanold) < TSDIFF) && (fabs(yrmean-yrmeanold) < YRDIFF)) fin = TRUE; } /* investigate at least minqts quartets */ if (n > minqts-2 && (fin || n > maxqts-2)) break; } /* round estimated numbers to 2 digits after the decimal point */ if (tserr != 0.0) tsmean = floor(100.0*tsmean+0.5)/100.0; if (yrerr != 0.0) yrmean = floor(100.0*yrmean+0.5)/100.0; /* update ML engine */ TSparam = tsmean; YRparam = yrmean; tranprobmat(); free_ivector(taxon); } /* optimization function TSparam - tree */ double opttst(double x) { double result; if (x < MINTS) TSparam = MINTS; else if (x > MAXTS) TSparam = MAXTS; else TSparam = x; tranprobmat(); /*epe*/ # if PARALLEL PP_Update_EEI(); # endif computedistan(); /* pre-set branchlengths = FALSE; parallel estimation = TRUE */ if (approxp_optn) result = usertree_alklhd(FALSE, TRUE); else result = usertree_lklhd(FALSE, TRUE); return (-result); } /* optimization function YRparam - tree */ double optyrt(double x) { double result; if (x < MINYR) YRparam = MINYR; else if (x > MAXYR) YRparam = MAXYR; else YRparam = x; tranprobmat(); /*epe*/ # if PARALLEL PP_Update_EEI(); # endif computedistan(); /* pre-set branchlengths = FALSE; parallel estimation = TRUE */ if (approxp_optn) result = usertree_alklhd(FALSE, TRUE); else result = usertree_lklhd(FALSE, TRUE); return (-result); } /* optimize substitution process parameters - tree */ void optimseqevolparamstree() { twodimenmin(EPSILON_SUBSTPARAM, (SH_optn || nuc_optn) && optim_optn && (data_optn == 0), MINTS, &TSparam, MAXTS, opttst, &tserr, (nuc_optn && TN_optn) && optim_optn && (data_optn == 0), MINYR, &YRparam, MAXYR, optyrt, &yrerr); } /* optimization function fracinv */ double optfi(double x) { double result; if (x < MINFI) fracinv = MINFI; else if (x > MAXFI) fracinv = MAXFI; else fracinv = x; /*epe*/ # if PARALLEL PP_Update_fracinv(); # endif computedistan(); /* pre-set branchlengths = FALSE; parallel estimation = TRUE */ if (approxp_optn) result = usertree_alklhd(FALSE, TRUE); else result = usertree_lklhd(FALSE, TRUE); return (-result); } /* optimization function Geta */ double optge(double x) { double result; if (x < MINGE) Geta = MINGE; else if (x > MAXGE) Geta = MAXGE; else Geta = x; updaterates(); /*epe*/ # if PARALLEL PP_Update_Rates(); # endif computedistan(); /* pre-set branchlengths = FALSE; parallel estimation = TRUE */ if (approxp_optn) result = usertree_alklhd(FALSE, TRUE); else result = usertree_lklhd(FALSE, TRUE); return (-result); } /* optimize rate heterogeneity parameters */ void optimrateparams() { twodimenmin(EPSILON_RATEPARAM, fracinv_optim, MINFI, &fracinv, fracconst, optfi, &fierr, grate_optim, MINGE, &Geta, MAXGE, optge, &geerr); } /******************************************************************************/ /* main routines to estimate parameters from tree or quartets */ /******************************************************************************/ /* estimate parameters of substitution process and rate heterogeneity - no tree n-taxon tree is not needed because of quartet method or NJ tree topology */ void estimateparametersnotree() { int it, nump, change; double TSold, YRold, FIold, GEold; it = 0; nump = 0; /* count number of parameters */ if (data_optn == NUCLEOTIDE && optim_optn) nump++; if (fracinv_optim || grate_optim) nump++; do { /* repeat until nothing changes any more */ it++; change = FALSE; /* optimize substitution parameters */ if (data_optn == NUCLEOTIDE && optim_optn) { TSold = TSparam; YRold = YRparam; /* * optimize */ fprintf(STDOUT, "Optimizing missing substitution process parameters\n"); fflush(STDOUT); if (qcalg_optn) { /* quartet sampling */ optimseqevolparamsquart(); } else { /* NJ tree */ tmpfp = tmpfile(); njtree(tmpfp); rewind(tmpfp); readusertree(tmpfp, FALSE); closefile(tmpfp); optimseqevolparamstree(); } /*epe*/ #if PARALLEL PP_NoUpdate(); # endif computedistan(); /* update ML distances */ /* same tolerance as 1D minimization */ if ((fabs(TSparam - TSold) > 3.3*EPSILON_SUBSTPARAM) || (fabs(YRparam - YRold) > 3.3*EPSILON_SUBSTPARAM) ) change = TRUE; } /* optimize rate heterogeneity variables */ if (fracinv_optim || grate_optim) { FIold = fracinv; GEold = Geta; /* * optimize */ fprintf(STDOUT, "Optimizing missing rate heterogeneity parameters\n"); fflush(STDOUT); /* compute NJ tree */ tmpfp = tmpfile(); njtree(tmpfp); /* use NJ tree topology to estimate parameters */ rewind(tmpfp); readusertree(tmpfp, FALSE); closefile(tmpfp); optimrateparams(); # if PARALLEL PP_NoUpdate(); # endif /* PARALLEL */ computedistan(); /* update ML distances */ /* same tolerance as 1D minimization */ if ((fabs(fracinv - FIold) > 3.3*EPSILON_RATEPARAM) || (fabs(Geta - GEold) > 3.3*EPSILON_RATEPARAM) ) change = TRUE; } if (nump == 1) return; } while (it != MAXITS && change); return; } /* estimateparametersnotree */ /* estimate parameters of substitution process and rate heterogeneity - tree same as above but here the n-taxon tree is already in memory */ void estimateparameterstree() { int it, nump, change; double TSold, YRold, FIold, GEold; it = 0; nump = 0; /* count number of parameters */ if (data_optn == NUCLEOTIDE && optim_optn) nump++; if (fracinv_optim || grate_optim) nump++; do { /* repeat until nothing changes any more */ it++; change = FALSE; /* optimize substitution process parameters */ if (data_optn == NUCLEOTIDE && optim_optn) { TSold = TSparam; YRold = YRparam; /* * optimize */ fprintf(STDOUT, "Optimizing missing substitution process parameters\n"); fflush(STDOUT); optimseqevolparamstree(); /*epe*/ /*??? - auskommentiert, HAS ;-) */ #ifdef EPE_DEBUG fprintf(STDOUT, "\n\nRED ALERT\n\n\n"); #endif /* EPE_DEBUG */ computedistan(); /* update ML distances */ /* same tolerance as 1D minimization */ if ((fabs(TSparam - TSold) > 3.3*EPSILON_SUBSTPARAM) || (fabs(YRparam - YRold) > 3.3*EPSILON_SUBSTPARAM) ) change = TRUE; } /* optimize rate heterogeneity variables */ if (fracinv_optim || grate_optim) { FIold = fracinv; GEold = Geta; /* * optimize */ fprintf(STDOUT, "Optimizing missing rate heterogeneity parameters\n"); fflush(STDOUT); optimrateparams(); /*epe*/ /*??? - auskommentiert, HAS ;-) */ #ifdef EPE_DEBUG fprintf(STDOUT, "\n\nRED ALERT\n\n\n"); #endif /* EPE_DEBUG */ computedistan(); /* update ML distances */ /* same tolerance as 1D minimization */ if ((fabs(fracinv - FIold) > 3.3*EPSILON_RATEPARAM) || (fabs(Geta - GEold) > 3.3*EPSILON_RATEPARAM) ) change = TRUE; } if (nump == 1) return; } while (it != MAXITS && change); return; } /* estimateparameterstree */ tree-puzzle-5.2/src/split.c0000644000076400001440000004601210073365313011421 /* * split.c (obsolete) * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ /* initialize tree with the following starting configuration (see pstep.h) */ void inittree_split(ONEEDGE **edge, /* out: new array of edges */ int **edgeofleaf,/* out: array of external edge ptrs */ int *rootleaf, /* out: rooting leaf (=trueID[0]) */ int Maxspc, /* in: Number of species (n) */ int Maxbrnch, /* in: Number of branches (2n-3) */ int *nextedge, /* out: next free edge index (=3) */ int *nextleaf, /* out: next free leaf index (=3) */ int *trueID) { int i, j; ONEEDGE *tmpedge; int *tmpedgeofleaf; /* allocate the memory for the whole tree */ /* allocate memory for vector with all the edges of the tree */ tmpedge = (ONEEDGE *) calloc((size_t) Maxbrnch, sizeof(ONEEDGE) ); if (tmpedge == NULL) maerror("edge in inittree"); *edge = tmpedge; /* allocate memory for tmpvector with edge numbers of leaves */ tmpedgeofleaf = (int *) calloc((size_t) Maxspc, sizeof(int) ); if (tmpedgeofleaf == NULL) maerror("edgeofleaf in inittree"); for (j = 0; j < Maxspc; j++) tmpedgeofleaf[j]=-1; *edgeofleaf = tmpedgeofleaf; /* allocate memory for all the edges the split map */ for (i = 0; i < Maxbrnch; i++) { (tmpedge)[i].split = (int *) calloc((size_t) Maxspc, sizeof(int) ); if (tmpedge[i].split == NULL) maerror("split array in inittree"); (tmpedge)[i].taxon = -1; for (j = 0; j < Maxspc; j++) (tmpedge)[i].split[j]=-1; /* number all edges */ tmpedge[i].numedge = i; } /* initialize tree */ *nextedge = 3; *nextleaf = 3; /* init split vectors: */ /* for edge 0 */ (tmpedge[0].split)[0] = trueID[0]; /* leaf 0 above this edge */ tmpedge[0].upsize = 1; (tmpedge[0].split)[Maxspc-1] = trueID[1]; /* leaf 0 below this edge */ (tmpedge[0].split)[Maxspc-2] = trueID[2]; /* leaf 0 below this edge */ tmpedge[0].downsize = 2; /* for edge 1 */ (tmpedge[1].split)[0] = trueID[0]; /* leaf 0 above this edge */ (tmpedge[1].split)[1] = trueID[2]; /* leaf 0 above this edge */ tmpedge[1].upsize = 2; (tmpedge[1].split)[Maxspc-1] = trueID[1]; /* leaf 0 below this edge */ tmpedge[1].downsize = 1; /* for edge 2 */ (tmpedge[2].split)[0] = trueID[0]; /* leaf 0 above this edge */ (tmpedge[2].split)[1] = trueID[1]; /* leaf 0 above this edge */ tmpedge[2].upsize = 2; (tmpedge[2].split)[Maxspc-1] = trueID[2]; /* leaf 0 below this edge */ tmpedge[2].downsize = 1; /* interconnection */ tmpedge[0].up = NULL; tmpedge[0].downleft = &tmpedge[1]; tmpedge[0].downright = &tmpedge[2]; tmpedge[1].up = &tmpedge[0]; tmpedge[1].downleft = NULL; tmpedge[1].downright = NULL; tmpedge[2].up = &tmpedge[0]; tmpedge[2].downleft = NULL; tmpedge[2].downright = NULL; /* taxon IDs of leaves */ tmpedge[0].taxon = trueID[0]; tmpedge[1].taxon = trueID[1]; tmpedge[2].taxon = trueID[2]; /* edges of leaves */ tmpedgeofleaf[trueID[0]] = 0; tmpedgeofleaf[trueID[1]] = 1; tmpedgeofleaf[trueID[2]] = 2; /* uppest edge =: root edge*/ *rootleaf = trueID[0]; } /* inittree_split */ /******************/ /* free memory (to be called after inittree) */ void freetree_split(ONEEDGE *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc) /* No. of species */ { int i; /* free split vectors */ for (i = 0; i < 2 * Maxspc - 3; i++) { free(edge[i].split); } /* free tree topology */ free(edge); /* free external edge lookup vector */ free(edgeofleaf); } /* freetree_split */ /******************/ /* check edge splits (debugging) */ void check_split( ONEEDGE *edge, /* edge array */ int Maxspc, /* No. of species */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *permut) { int n,m; fprintf(stderr, "Permutation: "); for (m = 0; m %d != %d>\n", m, (edge[m].taxon >= 0) ? 'e' : 'i', edge[m].taxon, edge[m].upsize, edge[m].downsize, edge[m].upsize+edge[m].downsize, nextleaf); fprintf(stderr, " UP:"); for (n = 0; n %d == %d> OK\n", m, (edge[m].taxon >= 0) ? 'e' : 'i', edge[m].taxon, edge[m].upsize, edge[m].downsize, edge[m].upsize+edge[m].downsize, nextleaf); } } } /* check_split */ /******************/ /* update splits after insertion */ void updatesplit_split(ONEEDGE *curredge, /* current edge */ int wherefrom, /* direction to last curr. edge */ int newleaf, /* leaf to add to splits */ ONEEDGE *edge, /* edge array */ int Maxspc, /* No. of species */ int Maxbrnch, /* No. of branches */ int *edgeofleaf, /* ext. edge idx array */ int in_nextedge, /* next free edge idx */ int in_nextleaf) /* next free leaf idx */ { switch (wherefrom) { case UP: curredge->split[(curredge->upsize)++] = newleaf; /* leaf is up */ if (curredge->downright != NULL) { /* not leaf */ updatesplit_split(curredge->downright, UP, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); updatesplit_split(curredge->downleft, UP, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } else { /* nothing to do */ return; } break; case DOWNLEFT: curredge->split[Maxspc - ++(curredge->downsize)] = newleaf; /* leaf is down */ if (curredge->downright != NULL) { /* not leaf */ updatesplit_split(curredge->downright, UP, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } if (curredge->up != NULL) { /* not root */ if ((curredge->up)->downright == curredge) { updatesplit_split(curredge->up, DOWNRIGHT, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } else { updatesplit_split(curredge->up, DOWNLEFT, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } } break; case DOWNRIGHT: curredge->split[Maxspc - ++(curredge->downsize)] = newleaf; /* leaf is down */ if (curredge->downright != NULL) { /* not leaf */ updatesplit_split(curredge->downleft, UP, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } if ((curredge->up) != NULL) { /* not root */ if ((curredge->up)->downright == curredge) { updatesplit_split(curredge->up, DOWNRIGHT, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } else { updatesplit_split(curredge->up, DOWNLEFT, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } } break; } } /* updatesplit_split */ /******************/ /* add next leaf on the specified edge */ void updatetreesplits_split(int dockedge, /* dockedge */ int newleaf, /* leaf to add to splits */ ONEEDGE *edge, /* edge array */ int Maxspc, /* No. of species */ int *edgeofleaf, /* ext. edge idx array */ int in_nextedge, /* next free edge idx */ int in_nextleaf, /* next free leaf idx */ ivector permut) { int n; /* counter */ int wherefrom; /* direction to last edge */ ONEEDGE *curredge; /* edge array */ /* copy clusters from dockedge to in_nextedge */ /* up-cluster: upsize-1 .. 0 */ for (n=(edge[dockedge].upsize) - 1; n >= 0; n--) { (edge[in_nextedge]).split[n] = (edge[dockedge]).split[n]; } (edge[in_nextedge]).upsize = (edge[dockedge]).upsize; /* down-cluster: downsize .. Maxspc-1 */ for (n=Maxspc - (edge[dockedge]).downsize; n < Maxspc; n++) { (edge[in_nextedge]).split[n] = (edge[dockedge]).split[n]; } (edge[in_nextedge]).downsize = (edge[dockedge]).downsize; /* add the new taxon to in_nextedge */ (edge[in_nextedge]).split[Maxspc - ++((edge[in_nextedge]).downsize)] = permut[in_nextleaf]; /* setup clusters for new external edge (in_nextedge+1) */ /* up-cluster: all taxa in tree */ for (n=0; n < in_nextleaf; n++) { (edge[in_nextedge+1]).split[n] = permut[n]; } (edge[in_nextedge+1]).upsize = in_nextleaf; /* down-cluster: the new taxon itself */ (edge[in_nextedge+1]).split[Maxspc-1] = permut[in_nextleaf]; (edge[in_nextedge+1]).downsize = 1; curredge = &(edge[in_nextedge]); if (curredge->up != NULL) { /* not root */ if (((curredge->up)->downright) == curredge) { wherefrom = DOWNRIGHT; } else { wherefrom = DOWNLEFT; } /* climbing up from insertion point */ updatesplit_split(curredge->up, wherefrom, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } /* climbing down to dockedge from insertion point */ updatesplit_split(&(edge[dockedge]), UP, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } /* updatetreesplits_split */ /******************/ /* add next leaf on the specified edge */ void addnextleaf_split(int dockedge, /* insert here */ ONEEDGE *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int rootleaf, /* uppest leaf */ int Maxspc, /* No. of species */ int Maxbrnch, /* No. of branches */ int *in_nextedge, /* next free edge idx */ int *in_nextleaf, /* next free leaf idx */ ivector permut) { int nextedge; int nextleaf; nextedge=*in_nextedge; nextleaf=*in_nextleaf; if (dockedge >= nextedge) { /* Trying to add leaf nextleaf to nonexisting edge dockedge */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR F TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } if (nextleaf >= Maxspc) { /* Trying to add leaf nextleaf to a tree with Maxspc leaves */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR G TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } /* necessary change in edgeofleaf if dockedge == root edge */ if (edgeofleaf[rootleaf] == dockedge) edgeofleaf[rootleaf] = nextedge; /* adding nextedge to the tree */ edge[nextedge].up = edge[dockedge].up; edge[nextedge].downleft = &edge[dockedge]; edge[nextedge].downright = &edge[nextedge+1]; edge[dockedge].up = &edge[nextedge]; /* if not root edge: connect ancestor to internal edge (nextedge) */ if (edge[nextedge].up != NULL) { if ( ((edge[nextedge].up)->downleft) == &edge[dockedge] ) (edge[nextedge].up)->downleft = &edge[nextedge]; else (edge[nextedge].up)->downright = &edge[nextedge]; } /* adding new external edge (nextedge+1) to the tree */ edge[nextedge+1].up = &edge[nextedge]; edge[nextedge+1].downleft = NULL; edge[nextedge+1].downright = NULL; edge[nextedge+1].taxon = permut[nextleaf]; edgeofleaf[permut[nextleaf]] = nextedge+1; updatetreesplits_split(dockedge, permut[nextleaf], edge, Maxspc, edgeofleaf, nextedge, nextleaf, permut); (*in_nextedge) += 2; (*in_nextleaf) ++; } /* addnextleaf */ /******************/ /* compute edge penalties using splits, if #minedges>1 choose one randomly */ void computepenalties_split(ONEEDGE *tmpedge, /* edge array */ int nextedge, /* next free edge idx */ int Maxspc, /* number of taxa */ ulimatrix neighbormatr, /* neighborhood matrix */ int *minedges, /* minimum edge vector */ int *out_howmany, /* number minimum edge */ uli *out_minpenalty, /* minimum penalty */ int *out_minedge) /* minimum edge */ { int i; /* counter */ int a, b; int idxA, idxB; int maxUP; /* index counter for right/left split cluster */ int howmany = 0; uli minpenalty; for (i = 0; i < nextedge; i++) { (tmpedge[i]).edgeinfo = 0; /* reset penalty */ maxUP = (tmpedge[i]).upsize; for (idxB = Maxspc - (tmpedge[i]).downsize; idxB < Maxspc; idxB++) { b = (tmpedge[i].split)[idxB]; for (idxA = 0; idxA < maxUP; idxA++) { a = (tmpedge[i].split)[idxA]; (tmpedge[i]).edgeinfo += neighbormatr[a][b]; } /* for all root-sided (up) taxa */ } /* for all non-root-sided (down) taxa */ if (howmany == 0) { /* first edge: init */ minedges[howmany++] = i; minpenalty = tmpedge[i].edgeinfo; } else { /* -> all other edges */ if (minpenalty == tmpedge[i].edgeinfo) { /* another min edge */ minedges[howmany++] = i; } else { /* -> not same minimum */ if (minpenalty > tmpedge[i].edgeinfo) { /* new minimum penalty */ howmany = 0; minedges[howmany++] = i; minpenalty = tmpedge[i].edgeinfo; } /* if new minimum */ } /* same minimum */ } /* if all other edges */ } /* for all edges */ *out_howmany = howmany, *out_minpenalty = minpenalty; if (howmany > 1) *out_minedge = minedges[randominteger(howmany)]; else *out_minedge = minedges[0]; } /* computepenalties_split */ /******************/ /* trueID-ed (HAS) */ /* perform one single puzzling step to produce one intermediate tree */ void onepstep_split( /* PStep (intermediate) tree topol: */ ONEEDGE **edge, /* out: new array of edges */ int **edgeofleaf, /* out: array of extern edge ptrs */ int *rootleaf, /* out: root leaf in topol, starting perm[0] */ unsigned char *quartettopols, /* in: quartetblock with all topols */ int Maxspc, /* in: Number of species (n) */ ivector permut) /* in: species permutation (trueID) */ { /* local variables: */ int Maxbrnch = (2*Maxspc)-3; /* Number of branches (2n-3) */ int nextedge; /* next free edge index (=3) */ int nextleaf; /* next free leaf index (=3) */ int minedge; /* insertion edge of minimum penalty */ uli mininfo; /* minimum penalty */ int a, b, c, i; /* quartet leaves, i to be inserted */ int idxA, idxB; int idxC, idxI; /* index counter for quartet leaves */ int chooseX, chooseY; /* end leaves of penalty path */ ONEEDGE *tmpedge; /* new array of edges */ int *tmpedgeofleaf; /* array of extern edge ptrs */ int tmprootleaf; /* root edge */ ulimatrix neighbormatr; int *minedges; int howmany; minedges = (int *) calloc((size_t) Maxspc, sizeof(int)); if (minedges == NULL) maerror("minimal edge set in onepstep_split"); neighbormatr = new_ulimatrix(Maxspc,Maxspc); /* allocate and initialize new tree topology */ inittree_split(&tmpedge, &tmpedgeofleaf, &tmprootleaf, Maxspc, Maxbrnch, &nextedge, &nextleaf, permut); for (idxI = 3; idxI < Maxspc; idxI++) { i = permut[idxI]; /* initialize penalty neighborhood matrix */ for (idxA = 0; idxA < nextleaf - 1; idxA++) { a = permut[idxA]; for (idxB = idxA + 1; idxB < nextleaf; idxB++) { b = permut[idxB]; neighbormatr[a][b] = 0; neighbormatr[b][a] = 0; } } /* for all entries in the upper neighbormatr */ /* * core of quartet puzzling algorithm */ for (idxA = 0; idxA < nextleaf - 2; idxA++) { a = permut[idxA]; for (idxB = idxA + 1; idxB < nextleaf - 1; idxB++) { b = permut[idxB]; for (idxC = idxB + 1; idxC < nextleaf; idxC++) { c = permut[idxC]; /* check which two leaves out of a,b,c are closer related to each other than to leaf i according to a least squares fit of the continous Bayesian weights to the seven trivial "attractive regions". We assign a score of 1 to all edges on the penalty path between these two leaves chooseX and chooseY */ /* de-trueID-ed (HAS) */ checkquartet(a, b, c, i, &chooseX, &chooseY); (neighbormatr[chooseX][chooseY])++; } /* for all quartets q=(a,b,c,i): c */ } /* for all quartets q=(a,b,c,i): b */ } /* for all quartets q=(a,b,c,i): a */ /* symetrize penalty neighborhood matrix */ for (idxA = 0; idxA < nextleaf - 1; idxA++) { a = permut[idxA]; for (idxB = idxA + 1; idxB < nextleaf; idxB++) { b = permut[idxB]; neighbormatr[a][b] += neighbormatr[b][a]; neighbormatr[b][a] = neighbormatr[a][b]; } } /* for all entries in the upper neighbormatr */ computepenalties_split(tmpedge, nextedge, Maxspc, neighbormatr, minedges, &howmany, &mininfo, &minedge); /* add the next leaf on minedge */ addnextleaf_split(minedge, tmpedge, tmpedgeofleaf, tmprootleaf, Maxspc, Maxbrnch, &nextedge, &nextleaf, permut); } /* adding all other leafs */ *edge = tmpedge; /* export tree topology */ *edgeofleaf = tmpedgeofleaf; /* export array of extern edge ptrs */ *rootleaf = tmprootleaf; /* export root edge */ free(minedges); free_ulimatrix(neighbormatr); } /* onepstep_split */ tree-puzzle-5.2/src/puzzle.h0000644000076400001440000007555510073365325011645 /* * puzzle.h * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifndef _PUZZLE_ #define _PUZZLE_ #ifndef PACKAGE # define PACKAGE "tree-puzzle" #endif #ifndef VERSION # define VERSION "5.2-generic" #endif #define DATE "July 2004" /* prototypes */ #include #include #include #include #include #include #include #include #include "pstep.h" #include "util.h" #include "ml.h" #include "consensus.h" #include "treesort.h" #ifdef PARALLEL # include "ppuzzle.h" #endif #define STDOUT stdout /* time check interval in seconds for ML/puzzling step status (900 = 15min) */ # define TIMECHECK_INTERVAL 900 /* filenames */ # define FILENAMELENGTH 2048 /* maximum exp difference, such that 1.0+exp(-TP_MAX_EXP_DIFF) == 1.0 */ # define TP_MAX_EXP_DIFF 40 # define INFILEDEFAULT "infile" # define OUTFILEDEFAULT "outfile" # define TREEFILEDEFAULT "outtree" # define INTREEDEFAULT "intree" # define DISTANCESDEFAULT "outdist" # define TRIANGLEDEFAULT "outlm.eps" # define UNRESOLVEDDEFAULT "outqlist" # define ALLQUARTDEFAULT "outallquart" # define ALLQUARTLHDEFAULT "outallquartlh" # define SITELHDEFAULT "outsitelh" # define SITELHBDEFAULT "outsitelhb" # define SITERATEDEFAULT "outsiterate" # define SITERATEBDEFAULT "outsiterateb" # define OUTPARAMDEFAULT "outparam" # define SUBSETDEFAULT "insubsetmatr" # define OUTPTLISTDEFAULT "outpstep" # define OUTPTORDERDEFAULT "outptorder" # define INFILE infilename # define OUTFILE outfilename # define TREEFILE outtreename # define INTREE intreename # define DISTANCES outdistname # define TRIANGLE outlmname # define UNRESOLVED outqlistname # define ALLQUART outallquartname # define ALLQUARTLH outallquartlhname # define SITELH outsitelhname # define SITELHB outsitelhbname # define SITERATE outsiteratename # define SITERATEB outsiteratebname # define OUTPARAM outparamname # define SUBSET insubsetmatrname # define OUTPTLIST outpstepname # define OUTPTORDER outptordername # define FILEPREFIX fileprefixname EXTERN char infilename [FILENAMELENGTH]; EXTERN char outfilename [FILENAMELENGTH]; EXTERN char outtreename [FILENAMELENGTH]; EXTERN char intreename [FILENAMELENGTH]; EXTERN char outdistname [FILENAMELENGTH]; EXTERN char outlmname [FILENAMELENGTH]; EXTERN char outqlistname [FILENAMELENGTH]; EXTERN char outallquartname [FILENAMELENGTH]; EXTERN char outallquartlhname [FILENAMELENGTH]; EXTERN char outsitelhname [FILENAMELENGTH]; EXTERN char outsitelhbname [FILENAMELENGTH]; EXTERN char outsiteratename [FILENAMELENGTH]; EXTERN char outsiteratebname [FILENAMELENGTH]; EXTERN char outparamname [FILENAMELENGTH]; EXTERN char insubsetmatrname [FILENAMELENGTH]; EXTERN char outpstepname [FILENAMELENGTH]; EXTERN char outptordername [FILENAMELENGTH]; EXTERN char fileprefixname [FILENAMELENGTH]; #define OUTFILEEXT "puzzle" #define TREEFILEEXT "tree" #define DISTANCESEXT "dist" #define TRIANGLEEXT "eps" #define UNRESOLVEDEXT "qlist" #define ALLQUARTEXT "allquart" #define ALLQUARTLHEXT "allquartlh" #define SITELHEXT "sitelh" #define SITELHBEXT "sitelhb" #define SITERATEEXT "siterate" #define SITERATEBEXT "siterateb" #define OUTPARAMEXT "param" #define SUBSETEXT "subsetmatr" #define OUTPTLISTEXT "pstep" #define OUTPTORDEREXT "ptorder" /* resetprefix values (xxx) */ #define RESET_NONE 0 #define RESET_INFILE 1 #define RESET_INTREE 2 /* setprefix_optn values (xxx) */ #define SETPREFIX_NONE 0 #define SETPREFIX_INFILE 1 #define SETPREFIX_INTREE 2 #define SETPREFIX_RESET 3 #define SETPREFIX_PREFIX 4 /* auto_aamodel/auto_datatype values (xxx) */ #define AUTO_OFF 0 #define AUTO_GUESS 1 #define AUTO_DEFAULT 2 /* qptlist values (xxx) */ #define PSTOUT_NONE 0 #define PSTOUT_ORDER 1 #define PSTOUT_LISTORDER 2 #define PSTOUT_LIST 3 /* dtat_optn values (xxx) */ #define NUCLEOTIDE 0 #define AMINOACID 1 #define BINARY 2 /* typ_optn values (xxx) */ #define TREERECON_OPTN 0 #define LIKMAPING_OPTN 1 #define NUMTYPES 2 /* puzzlemodes (xxx) */ #define QUARTPUZ 0 #define USERTREE 1 #define CONSENSUS 2 #define PAIRDIST 3 #define NUMPUZZLEMODES 4 /* modes for rootsearch (xxx) */ #define ROOT_USER 0 #define ROOT_AUTO 1 #define ROOT_DISPLAYED 2 #define NUMROOTSEARCH 3 #if 0 /* rhetmodes (xxx) Modes of rate heterogeneity */ #define UNIFORMRATE 0 #define GAMMARATE 1 #define TWORATE 2 #define MIXEDRATE 3 #endif /* defines for types of quartet likelihood computation (xxx) */ #define EXACT 0 #define APPROX 1 /* defines for results of sequence number check (seqnumcheck) */ #define SEQNUM_OK 0 #define SEQNUM_TOOFEW 1 #define SEQNUM_TOOMANY 2 #if 0 typedef struct { uli fullres_pro; uli fullres_con; uli partres_pro; uli partres_con; uli unres; uli missing; uli qsum; } qsupportarr_t; EXTERN cmatrix biparts; /* bipartitions of tree of current puzzling step */ EXTERN cmatrix consbiparts; /* bipartitions of majority rule consensus tree */ EXTERN int xsize; /* depth of consensus tree picture */ EXTERN ivector consconfid; /* confidence values of majority rule consensus tree */ EXTERN ivector conssizes; /* partition sizes of majority rule consensus tree */ EXTERN ivector xcor; /* x-coordinates of consensus tree nodes */ EXTERN ivector ycor; /* y-coordinates of consensus tree nodes */ EXTERN ivector ycormax; /* maximal y-coordinates of consensus tree nodes */ EXTERN ivector ycormin; /* minimal y-coordinates of consensus tree nodes */ /* splits for consensus */ EXTERN int splitlength; /* length of one entry in splitpatterns */ EXTERN uli maxbiparts; /* memory reserved for maxbiparts bipartitions */ EXTERN uli numbiparts; /* number of different bipartitions */ EXTERN int *splitsizes; /* size of all different splits of all trees */ EXTERN uli *splitcomptemp; /* temp variable to compress bipartitions coding */ EXTERN uli *splitfreqs; /* frequencies of different splits of all trees */ EXTERN uli *splitpatterns; /* all different splits of all trees */ EXTERN qsupportarr_t *qsupportarr; /* quartet support values per split */ EXTERN uli consincluded; /* number of included biparts in the consensus tree */ EXTERN uli consfifty; /* number of biparts >= 50% */ EXTERN uli conscongruent; /* number of first incongruent bipart */ #endif /* variables */ EXTERN cmatrix Seqchars; /* characters contained in data set */ EXTERN ivector Seqgapchar; /* counter for gaps contained in sequence */ EXTERN ivector Seqotherchar; /* counter for ambiguous contained in sequence */ EXTERN cmatrix treepict; /* picture of consensus tree */ EXTERN double minscore; /* value of edgescore on minedge */ EXTERN double tstvf84; /* F84 transition/transversion ratio */ EXTERN double tstvratio; /* expected transition/transversion ratio */ EXTERN double yrtsratio; /* expected pyrimidine/purine transition ratio */ EXTERN dvector ulkl; /* log L of user trees */ EXTERN dmatrix allsites; /* log L per sites of utrees (numutrees,Numptrn) */ EXTERN dvector ulklc; /* log L of utrees (clock) (numutrees,Numptrn) */ EXTERN dmatrix allsitesc; /* log L per sites of user trees (clock) */ EXTERN FILE *utfp; /* pointer to user tree file */ EXTERN FILE *ofp; /* pointer to output file */ EXTERN FILE *seqfp; /* pointer to sequence input file */ EXTERN FILE *tfp; /* pointer to tree file */ EXTERN FILE *dfp; /* pointer to distance file */ EXTERN FILE *trifp; /* pointer to triangle file */ EXTERN FILE *unresfp; /* pointer to file with unresolved quartets */ EXTERN FILE *tmpfp; /* pointer to temporary file */ EXTERN FILE *qptlist; /* pointer to file with puzzling step trees */ EXTERN FILE *qptorder; /* pointer to file with unique puzzling step trees */ EXTERN int SHcodon; /* whether SH should be applied to 1st, 2nd codon positions */ EXTERN int utree_optn; /* use first user tree for estimation */ EXTERN int listqptrees; /* list puzzling step trees */ EXTERN int approxqp; /* approximate QP quartets */ EXTERN int codon_optn; /* declares what positions in a codon should be used */ EXTERN int compclock; /* computation of clocklike branch lengths */ EXTERN int chooseA; /* leaf variable */ EXTERN int chooseB; /* leaf variable */ EXTERN int clustA, clustB, clustC, clustD; /* number of members of LM clusters */ EXTERN int Frequ_optn; /* use empirical base frequencies */ /* PSTEP_ORIG_H */ EXTERN int Maxbrnch; /* 2*Maxspc - 3 */ EXTERN int Maxseqc; /* number of sequence characters per taxum */ EXTERN int mflag; /* flag used for correct printing of runtime messages */ EXTERN int numclust; /* number of clusters in LM analysis */ EXTERN int outgroup; /* outgroup */ EXTERN int puzzlemode; /* computation of QP tree and/or ML distances */ EXTERN int rootsearch; /* how location of root is found */ EXTERN int rhetmode; /* model of rate heterogeneity */ EXTERN int seqnumcheck; /* result of sequence number checkheterogeneity */ EXTERN int usebestq_optn; /* use only best quartet topology, no bayesian weights */ EXTERN int printrmatr_optn; /* print rate matrix to screen */ EXTERN int usebranch_optn; /* use branch lengths given in usertree */ EXTERN int show_optn; /* show unresolved quartets */ EXTERN int savequart_optn; /* save memory block which quartets to file */ EXTERN int savequartlh_optn; /* save quartet likelihoods to file */ EXTERN int saveqlhbin_optn; /* save quartet likelihoods binary */ EXTERN int savesitelh_optn; /* save site likelihoods (PHILIP-like) */ EXTERN int savesitelhb_optn; /* save site likelihoods (binary) */ EXTERN int savesiterate_optn; /* save site rates (PHILIP-like) */ EXTERN int savesiterateb_optn; /* save site rates (binary) */ EXTERN int readquart_optn; /* read memory block which quartets from file */ EXTERN int fixedorder_optn; /* use fixed puzzling insert order 1,2,3,...n */ #if 0 EXTERN int skipmlbranch_optn;/* skip ml branches in final tree */ #endif EXTERN int conssub50_optn; /* do consensus down to percentage of first incongruence/ambiguity */ EXTERN int qsupport_optn; /* compute quartet support for the splits */ EXTERN int dotreetest_optn; /* compute tree statistics (ELW, KH, SH) */ EXTERN int dotreelh_optn; /* compute lh/branch lengths (QP,consensus) */ EXTERN int setprefix_optn; /* use other FILEPREFIX that INFILENAME */ EXTERN int consensus_optn; /* do consensus tree instead of user trees */ EXTERN int sym_optn; /* symmetrize doublet frequencies */ EXTERN int ytaxcounter; /* counter for establishing y-coordinates of all taxa */ EXTERN int numutrees; /* number of users trees in input tree file */ EXTERN ivector clusterA, clusterB, clusterC, clusterD; /* clusters for LM analysis */ EXTERN ivector ycortax; /* y-coordinates of all taxa */ EXTERN uli badqs; /* number of bad quartets */ EXTERN uli unresqs; /* number of unresolved quartets, formerly badqs */ EXTERN uli partresqs; /* number of partly resolved quartets */ EXTERN uli fullresqs; /* number of fully resolved quartets */ EXTERN uli missingqs; /* number of fully resolved quartets */ EXTERN ulivector badtaxon; /* involment of each taxon in a bad quartet */ EXTERN ulimatrix qinfomatr; /* sums of quartet topologies per taxon [0]=sum */ EXTERN uli Currtrial; /* counter for puzzling steps */ EXTERN uli Numquartets; /* number of quartets */ EXTERN uli Numtrial; /* number of puzzling steps */ EXTERN uli lmqts; /* quartets investigated in LM analysis (0 = ALL) */ EXTERN int auto_datatype; /* guess datatype ? */ EXTERN int guessdata_optn; /* guessed datatype */ EXTERN int auto_aamodel; /* guess amino acid modell ? */ EXTERN int guessauto_aamodel; /* guessed amino acid modell ? */ EXTERN int guessDayhf_optn; /* guessed Dayhoff model option */ EXTERN int guessJtt_optn; /* guessed JTT model option */ EXTERN int guessblosum62_optn; /* guessed BLOSUM 62 model option */ EXTERN int guessmtrev_optn; /* guessed mtREV model option */ EXTERN int guesscprev_optn; /* guessed cpREV model option */ EXTERN int guessvtmv_optn; /* guessed VT model option */ EXTERN int guesswag_optn; /* guessed WAG model option */ /* missing data: for handling subsets */ EXTERN int readsubset_optn; /* guessed WAG model option */ EXTERN int Maxsubset; /* number of subsets */ EXTERN imatrix ss_setovlgraph; /* size of overlap >= 3 between 2 subsets */ EXTERN imatrix ss_setoverlaps; /* size of overlap between 2 subsets */ EXTERN imatrix ss_setovllist; /* list with ovlerlapping subsets */ EXTERN ivector ss_setovllistsize; /* size of list with ovlerlapping subsets */ EXTERN imatrix ss_matrix; /* boolean list: taxon in set? */ EXTERN imatrix ss_list; /* list of taxa in set */ EXTERN ivector ss_listsize; /* size of list with taxa */ /* counter variables needed in likelihood mapping analysis */ EXTERN uli ar1, ar2, ar3; EXTERN uli reg1, reg2, reg3, reg4, reg5, reg6, reg7; EXTERN uli reg1l, reg1r, reg2u, reg2d, reg3u, reg3d, reg4u, reg4d, reg5l, reg5r, reg6u, reg6d; EXTERN unsigned char *quartetinfo; /* place where quartets are stored */ EXTERN dvector qweight; /* for use in QP and LM analysis */ EXTERN dvector sqdiff; EXTERN ivector qworder; EXTERN ivector sqorder; EXTERN int randseed; EXTERN int psteptreestrlen; #if 0 typedef struct treelistitemtypedummy { struct treelistitemtypedummy *pred; struct treelistitemtypedummy *succ; struct treelistitemtypedummy *sortnext; struct treelistitemtypedummy *sortlast; char *tree; int count; int id; int idx; } treelistitemtype; EXTERN treelistitemtype *psteptreelist; EXTERN treelistitemtype *psteptreesortlist; EXTERN int psteptreenum; EXTERN int psteptreesum; #endif /* prototypes */ void makeF84model(void); void compnumqts(void); void setoptions(void); int openfiletoread(FILE **, char[], char[]); int openfiletowrite(FILE **, char[], char[]); int openfiletoappend(FILE **, char[], char[]); void closefile(FILE *); void symdoublets(void); void computeexpectations(void); void putdistance(FILE *); void findidenticals(FILE *); double averagedist(int maxspc, dmatrix distanmat, double *meandist, double *mindist, double *maxdist, double *stddevdist, double *vardist); void initps(FILE *); void plotlmpoint(FILE *, double, double); void finishps(FILE *); void makelmpoint(FILE *, double, double, double); void timestamp(FILE *); void writeoutputfile(FILE *, int); /* definitions for writing output */ #define WRITEALL 0 #define WRITEPARAMS 1 #define WRITEREST 2 void writetimesstat(FILE *ofp); void writecutree(FILE *, int); void starttimer(void); void checktimer(uli); /* void estimateparametersnotree(void); * moved to mlparam.c */ /* void estimateparameterstree(void); * moved to mlparam.c */ int main(int, char *[]); int ulicmp(const void *, const void *); int intcmp(const void *, const void *); void readid(FILE *, int); char readnextcharacter(FILE *, int, int); /* skip rest of the line */ void skiprestofline(FILE *ifp, /* input file stream */ int notu, /* taxon number - for error msg. */ int nsite); /* sequence position - for error msg. */ /* skip control characters and blanks */ void skipcntrl(FILE *ifp, /* input file stream */ int notu, /* taxon number - for error msg. */ int nsite); /* sequence position - for error msg. */ /* read sequences of one data set */ void getseqs(FILE *ifp, /* in: input file stream */ int Maxspc, /* in: number of taxa */ int Maxseqc, /* in: number of sites */ cmatrix *seqch, /* out: alignment matrix */ cmatrix identif); /* io: taxon names (10 char w/o stop) */ /* initialize identifer arrays */ void initid(int t, /* in: number of taxa */ cmatrix *identif, /* out: name array w/o end of string */ cmatrix *namestr); /* out: name array with end of string */ /* copy undelimited identifer array to '\0' delimited identifer array */ void identif2namestr(int num, /* number of taxa */ cmatrix Identif, /* non-delimited names */ cmatrix Namestr); /* proper delimited names */ void fputid10(FILE *, int); int fputid(FILE *, int); /* read first line of sequence data set */ void getsizesites(FILE *ifp, /* in: input file stream */ int *Maxspc, /* out: number of taxa */ int *Maxseqc); /* out: number of sites */ /* read alignment from file */ void readsequencefile(FILE *seqfp, /* in: sequence input file stream */ int *Maxspc, /* out: number of taxa */ int *Maxseqc, /* out: number of sites */ cmatrix *identif, /* out: name array w/o end of str */ cmatrix *namestr, /* out: name array with end of str */ cmatrix *Seqchars); /* out: alignment matrix */ /* read subsets from file */ void readsubsetfile(FILE *seqfp, /* in: sequence input file stream */ int Maxspc, /* in: number of taxa */ cmatrix namestr, /* in: names taxa (seq file) */ int *Maxsubset, /* out: number of subsets */ imatrix *ss_setovlgraph, /* out: size of overlap >= 3 between 2 subsets */ imatrix *ss_setoverlaps, /* out: size of overlap between 2 subsets */ imatrix *ss_setovllist, /* out: list with ovlerlapping subsets */ ivector *ss_setovllistsize, /* out: size of list with ovlerlapping subsets */ imatrix *ss_matrix, /* out: boolean list: taxon in set? */ imatrix *ss_list, /* out: list of taxa in set */ ivector *ss_listsize); /* out: size of list with taxa */ /* permute taxon order */ void permutetaxa_ss(int Maxspc, /* in: number of taxa */ ivector permutation, /* permuted taxon order */ cmatrix namestr, /* in: names taxa (seq file) */ int Maxsubset, /* out: number of subsets */ imatrix ss_setovlgraph,/* out: size of overlap >= 3 between 2 subsets */ imatrix ss_setoverlaps,/* out: size of overlap between 2 subsets */ imatrix ss_setovllist, /* out: list with overlapping subsets */ ivector ss_setovllistsize,/* out: size of list with ovlerlapping subsets */ imatrix ss_matrix, /* out: bool list: taxon in set? */ imatrix ss_list, /* out: list of taxa in set */ ivector ss_listsize); /* out: size of list with taxa */ /* print subsets */ void fprintfss(FILE *ofp, /* in: output file stream */ int Maxspc, /* in: number of taxa */ int Maxsubset, /* out: number of subsets */ imatrix ss_setovlgraph, /* out: size of overlap >= 3 between 2 subsets */ imatrix ss_setoverlaps, /* out: size of overlap between 2 subsets */ imatrix ss_setovllist, /* out: list with ovlerlapping subsets */ ivector ss_setovllistsize, /* out: size of list with ovlerlapping subsets */ imatrix ss_matrix, /* out: boolean list: taxon in set? */ imatrix ss_list, /* out: list of taxa in set */ ivector ss_listsize); /* out: size of list with taxa */ /* check connectedness of subsets */ void checkss(FILE *ofp, /* in: output file stream */ int Maxspc, /* in: number of taxa */ int Maxsubset, /* out: number of subsets */ imatrix ss_setovlgraph, /* out: size of overlap >= 3 between 2 subsets */ imatrix ss_setoverlaps, /* out: size of overlap between 2 subsets */ imatrix ss_setovllist, /* out: list with ovlerlapping subsets */ ivector ss_setovllistsize, /* out: size of list with ovlerlapping subsets */ imatrix ss_matrix, /* out: boolean list: taxon in set? */ imatrix ss_list, /* out: list of taxa in set */ ivector ss_listsize); /* out: size of list with taxa */ /* guess data type: NUCLEOTIDE:0, AMINOACID:1, BINARY:2 */ int guessdatatype(cmatrix Seqchars, /* alignment matrix (Maxspc x Maxseqc) */ int Maxspc, /* number of taxa */ int Maxseqc); /* number of sites */ void translatedataset(int maxspc, int maxseqc, int *maxsite, cmatrix seqchars, cmatrix *seqchar, ivector *seqgapchar, ivector *seqotherchar); void estimatebasefreqs(void); void guessmodel(void); #if 0 int *initctree(); void copytree_trueID(int *ctree, /* out: copy for effective sorting */ int *trueID, /* in: permutation vector */ ONEEDGE *edgeset, /* in: intermediate tree topology */ int *edgeofleaf, /* dito. */ int nextleaf); /* in: next free leaf (bound) */ void freectree(int **snodes); void printctree(int *ctree); char *sprintfctree(int *ctree, int strlen); void fprintffullpstree(FILE *outf, char *treestr); int printfsortctree(int *ctree); int sortctree(int *ctree); int ct_1stedge(int node); int ct_2ndedge(int node); int ct_3rdedge(int node); void printfpstrees(treelistitemtype *list); void printfsortedpstrees(treelistitemtype *list); void fprintfsortedpstrees(FILE *output, treelistitemtype *list, int itemnum, int itemsum, int comment, float cutoff); void sortbynum(treelistitemtype *list, treelistitemtype **sortlist); treelistitemtype *addtree2list(char **tree, int numtrees, treelistitemtype **list, int *numitems, int *numsum); void freetreelist(treelistitemtype **list, int *numitems, int *numsum); #endif #if 0 void resetedgeinfo(void); void incrementedgeinfo(int, int); void minimumedgeinfo(void); #endif #if 0 void initconsensus(void); /* recursive function to get bipartitions */ void makepart_trueID(int i, /* */ int curribrnch, /* in: current branch in traversal */ ONEEDGE *edge, /* in: tree topology */ int *edgeofleaf, /* in: ext. edge list */ int *trueID, /* in: permutation list */ cmatrix biparts, /* out: split strings, edge by edge */ int Maxspc); /* in: number of species in tree */ /* compute bipartitions of current puzzling step tree */ void computebiparts_trueID(ONEEDGE *edge, /* in: tree topology */ int *edgeofleaf, /* in: ext. edge list */ int *trueID, /* in: permutation list */ cmatrix biparts, /* out: splits */ int outgroup, /* in: outgroup of tree */ int Maxspc); /* in: number of taxa in tree */ void printsplit(FILE *, uli); void makenewsplitentries(cmatrix bip, /* in: split string vector */ int numspl, /* in: no. of new splits */ uli **in_splitpatterns,/* io: known compr splits */ int **in_splitsizes, /* io: kn. split sizes: '.'*/ uli **in_splitfreqs, /* io: kn. split frequences*/ uli *in_numbiparts, /* io: no. of splits so far*/ uli *in_maxbiparts, /* io: reserved memory */ int Maxspc); /* in: no. of species */ /* copy bipartition n of all different splitpatterns to consbiparts[k] */ void copysplit(uli n, uli *splitpatterns, int k, cmatrix consbipartsvec); void makeconsensus(uli, int); /* write node (writeconsensustree) */ void writenode(FILE *treefile, /* in: output stream */ int node, /* current node */ int qsupp_optn, /* 'print quartet support' flag */ qsupportarr_t *qsupparr, /* quartet support values */ int *column); /* current line position */ /* write consensus tree */ void writeconsensustree(FILE *treefile, /* in: output stream */ int qsupp_optn, /* 'print quartsupp' flag */ qsupportarr_t *qsupparr); /* quartet support values */ void writeconsensustree(FILE *, int, qsupportarr_t *); void nodecoordinates(int); void drawnode(int, int); void plotconsensustree(FILE *); #endif unsigned char *callocquartets(int); void freequartets(void); unsigned char readquartet(int, int, int, int); void writequartet(int, int, int, int, unsigned char); void sort3doubles(dvector, ivector); void computeallquartets(void); /* check the branching structure between the leaves (not the taxa!) A, B, C, and I (A, B, C, I don't need to be ordered). As a result, the two leaves that are closer related to each other than to leaf I are found in chooseX and chooseY. If the branching structure is not uniquely defined, chooseX and chooseY are chosen randomly from the possible taxa */ void checkquartet(int A, /* quartet taxon ID */ int B, /* dito. */ int C, /* dito. */ int I, /* dito., to be inserted */ int *chooseX, /* (chooseX,chooseY | x,I) */ int *chooseY); /* chooseX+Y are non-neighbors of I */ void checkquartet_trueID(int A, /* quartet leaf idx in permutation array */ int B, /* dito. */ int C, /* dito. */ int I, /* dito., to be inserted */ int *trueID, /* permutation array */ int *chooseX, /* (chooseX,chooseY | x,I) */ int *chooseY); /* chooseX+Y are non-neighbors of I */ void num2quart(uli qnum, int *a, int *b, int *c, int *d); uli numquarts(int maxspc); uli quart2num (int a, int b, int c, int d); void writetpqfheader(int nspec, FILE *ofp, int flag); /* extracted from main (xxx) */ void compute_quartlklhds(int a, int b, int c, int d, double *d1, double *d2, double *d3, int approx); /* definitions for timing */ #define OVERALL 0 #define GENERAL 1 #define OPTIONS 2 #define PARAMEST 3 #define QUARTETS 4 #define PUZZLING 5 #define TREEEVAL 6 typedef struct { int currentjob; clock_t tempcpu; clock_t tempfullcpu; clock_t tempcpustart; time_t temptime; time_t tempfulltime; time_t temptimestart; clock_t maxcpu; clock_t mincpu; time_t maxtime; time_t mintime; double maxcpublock; double mincpublock; double mincputick; double mincputicktime; double maxtimeblock; double mintimeblock; double generalcpu; double optionscpu; double paramestcpu; double quartcpu; double quartblockcpu; double quartmaxcpu; double quartmincpu; double puzzcpu; double puzzblockcpu; double puzzmaxcpu; double puzzmincpu; double treecpu; double treeblockcpu; double treemaxcpu; double treemincpu; double cpu; double fullcpu; double generaltime; double optionstime; double paramesttime; double quarttime; double quartblocktime; double quartmaxtime; double quartmintime; double puzztime; double puzzblocktime; double puzzmaxtime; double puzzmintime; double treetime; double treeblocktime; double treemaxtime; double treemintime; double time; double fulltime; } timearray_t; EXTERN double cputime, walltime; EXTERN double fullcpu, fulltime; EXTERN double fullcputime, fullwalltime; EXTERN double altcputime, altwalltime; EXTERN clock_t cputimestart, cputimestop, cputimedummy; EXTERN time_t walltimestart, walltimestop, walltimedummy; EXTERN clock_t Startcpu; /* start cpu time */ EXTERN clock_t Stopcpu; /* stop cpu time */ EXTERN time_t MLstepStarttime; /* start time */ EXTERN time_t MLstepStoptime; /* stop time */ EXTERN time_t PStepStarttime; /* start time */ EXTERN time_t PStepStoptime; /* stop time */ EXTERN time_t PEstStarttime; /* start time */ EXTERN time_t PEstStoptime; /* stop time */ EXTERN time_t Starttime; /* start time */ EXTERN time_t Stoptime; /* stop time */ EXTERN time_t time0; /* timer variable */ EXTERN time_t time1; /* yet another timer */ EXTERN time_t time2; /* yet another timer */ EXTERN timearray_t tarr; void resetqblocktime(timearray_t *ta); void resetpblocktime(timearray_t *ta); void inittimearr(timearray_t *ta); void addtimes(int jobtype, timearray_t *ta); #ifdef TIMEDEBUG void printtimearr(timearray_t *ta); #endif /* TIMEDEBUG */ /* compute Bayesian weights from log-lkls d1, d2, d3 */ unsigned char loglkl2weight(int a, int b, int c, int i, double d1, double d2, double d3, int usebestq); #if 0 #ifdef PARALLEL # include "ppuzzle.h" #endif #endif #endif /* _PUZZLE_ */ tree-puzzle-5.2/src/puzzle1.c0000644000076400001440000065747610074444162011727 /* * puzzle1.c * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #define USE_GTR 1 #ifdef HAVE_CONFIG_H # include #endif #if !PARALLEL # ifdef USE_CONSOLE_H # include # endif #endif #define EXTERN #include "puzzle.h" #include "gamma.h" #include "treetest.h" #if PARALLEL # include "ppuzzle.h" #endif /*epe*/ #ifdef VT # include #endif /******* debugging stuff - HAS ;-) ********/ int PPP1=0; /* fprintf(stderr, "PPP1: %d (%s:%d)\n", PPP1++, __FILE__, __LINE__); */ void fprintftimespan(FILE *ofp, time_t start, time_t stop, time_t allstart, char *comment) { double timespan; timespan = difftime(stop, start); fprintf(ofp, "TTT: %-25s took %.0f seconds (= %.1f minutes = %.1f hours)\n", comment, timespan, timespan/60., timespan/3600.); timespan = difftime(stop, allstart); fprintf(ofp, "TTT: from beginning: %.0f seconds (= %.1f minutes = %.1f hours)\n", timespan, timespan/60., timespan/3600.); fflush(ofp); } /******* end of debugging stuff - HAS ;-) ********/ void num2quart(uli qnum, int *a, int *b, int *c, int *d) { double temp; uli aa, bb, cc, dd; uli lowval=0, highval=0; aa=0; bb=1; cc=2; dd=3; temp = (double)(24 * qnum); temp = sqrt(temp); temp = sqrt(temp); /* temp = pow(temp, (double)(1/4)); */ dd = (uli) floor(temp) + 1; if (dd < 3) dd = 3; lowval = (uli) dd*(dd-1)*(dd-2)*(dd-3)/24; highval = (uli) (dd+1)*dd*(dd-1)*(dd-2)/24; if (lowval >= qnum) while ((lowval > qnum)) { dd -= 1; lowval = (uli) dd*(dd-1)*(dd-2)*(dd-3)/24; } else { while (highval <= qnum) { dd += 1; highval = (uli) (dd+1)*dd*(dd-1)*(dd-2)/24; } lowval = (uli) dd*(dd-1)*(dd-2)*(dd-3)/24; } qnum -= lowval; if (qnum > 0) { temp = (double)(6 * qnum); temp = pow(temp, (double)(1/3)); cc = (uli) floor(temp); if (cc < 2) cc= 2; lowval = (uli) cc*(cc-1)*(cc-2)/6; highval = (uli) (cc+1)*cc*(cc-1)/6; if (lowval >= qnum) while ((lowval > qnum)) { cc -= 1; lowval = (uli) cc*(cc-1)*(cc-2)/6; } else { while (highval <= qnum) { cc += 1; highval = (uli) (cc+1)*cc*(cc-1)/6; } lowval = (uli) cc*(cc-1)*(cc-2)/6; } qnum -= lowval; if (qnum > 0) { temp = (double)(2 * qnum); temp = sqrt(temp); bb = (uli) floor(temp); if (bb < 1) bb= 1; lowval = (uli) bb*(bb-1)/2; highval = (uli) (bb+1)*bb/2; if (lowval >= qnum) while ((lowval > qnum)) { bb -= 1; lowval = (uli) bb*(bb-1)/2; } else { while (highval <= qnum) { bb += 1; highval = (uli) (bb+1)*bb/2; } lowval = (uli) bb*(bb-1)/2; } qnum -= lowval; if (qnum > 0) { aa = (uli) qnum; if (aa < 0) aa= 0; } } } *d = (int)dd; *c = (int)cc; *b = (int)bb; *a = (int)aa; } /* num2quart */ /******************/ uli numquarts(int maxspc) { uli tmp; int a, b, c, d; if (maxspc < 4) return (uli)0; else { maxspc--; a = maxspc-3; b = maxspc-2; c = maxspc-1; d = maxspc; tmp = (uli) 1 + a + (uli) b * (b-1) / 2 + (uli) c * (c-1) * (c-2) / 6 + (uli) d * (d-1) * (d-2) * (d-3) / 24; return (tmp); } } /* numquarts */ /******************/ uli quart2num (int a, int b, int c, int d) { uli tmp; if ((a>b) || (b>c) || (c>d)) { fprintf(stderr, "Error PP5 not (%d <= %d <= %d <= %d) !!!\n", a, b, c, d); # if PARALLEL PP_Finalize(); # endif exit (1); } tmp = (uli) a + (uli) b * (b-1) / 2 + (uli) c * (c-1) * (c-2) / 6 + (uli) d * (d-1) * (d-2) * (d-3) / 24; return (tmp); } /* quart2num */ /******************/ /* flag=0 old allquart binary */ /* flag=1 allquart binary */ /* flag=2 allquart ACSII */ /* flag=3 quartlh binary */ /* flag=4 quartlh ASCII */ void writetpqfheader(int nspec, FILE *ofp, int flag) { int currspec; if (flag == 0) { unsigned long nquart; unsigned long blocklen; nquart = numquarts(nspec); /* compute number of bytes */ if (nquart % 2 == 0) { /* even number */ blocklen = (nquart)/2; } else { /* odd number */ blocklen = (nquart + 1)/2; } /* fprintf(STDOUT, "Writing quartet file: %s\n", filename); */ fprintf(ofp, "TREE-PUZZLE\n%s\n\n", VERSION); fprintf(ofp, "species: %d\n", nspec); fprintf(ofp, "quartets: %lu\n", nquart); fprintf(ofp, "bytes: %lu\n\n", blocklen); /* fwrite(&(quartetinfo[0]), sizeof(char), blocklen, ofp); */ } if (flag == 1) fprintf(ofp, "##TPQF-BB (TREE-PUZZLE %s)\n%d\n", VERSION, nspec); if (flag == 2) fprintf(ofp, "##TPQF-BA (TREE-PUZZLE %s)\n%d\n", VERSION, nspec); if (flag == 3) fprintf(ofp, "##TPQF-LB (TREE-PUZZLE %s)\n%d\n", VERSION, nspec); if (flag == 4) fprintf(ofp, "##TPQF-LA (TREE-PUZZLE %s)\n%d\n", VERSION, nspec); for (currspec=0; currspec MAXTS) { fprintf(STDOUT, "\n\n\nF84 model not possible "); fprintf(STDOUT, "(bad Ts/Tv parameter)\n"); tstvf84 = 0.0; return; } if (yr < MINYR || yr > MAXYR) { fprintf(STDOUT, "\n\n\nF84 model not possible "); fprintf(STDOUT, "(bad Y/R transition parameter)\n"); tstvf84 = 0.0; return; } TSparam = ts; YRparam = yr; optim_optn = FALSE; } /* makeF84model */ /* compute number of quartets used in LM analysis */ void compnumqts() { if (lmqts == 0) { if (numclust == 4) Numquartets = (uli) clustA*clustB*clustC*clustD; if (numclust == 3) Numquartets = (uli) clustA*clustB*clustC*(clustC-1)/2; if (numclust == 2) Numquartets = (uli) clustA*(clustA-1)/2 * clustB*(clustB-1)/2; if (numclust == 1) Numquartets = (uli) Maxspc*(Maxspc-1)*(Maxspc-2)*(Maxspc-3)/24; } else { Numquartets = lmqts; } } /* compnumqts */ /* set options interactively */ void setoptions() { int i, valid; double sumfreq; char ch; /* defaults */ rhetmode = UNIFORMRATE; /* assume rate homogeneity */ numcats = 1; Geta = 0.05; grate_optim = FALSE; fracinv = 0.0; fracinv_optim = FALSE; compclock = FALSE; /* compute clocklike branch lengths */ locroot = -1; /* search for optimal place of root */ qcalg_optn = FALSE; /* don't use sampling of quartets */ approxp_optn = TRUE; /* approximate parameter estimates */ listqptrees = PSTOUT_NONE; /* list puzzling step trees */ /* approximate QP quartets? */ if (Maxspc <= 6) approxqp = FALSE; else approxqp = TRUE; codon_optn = 0; /* use all positions in a codon */ /* number of puzzling steps */ if (Maxspc <= 25) Numtrial = 1000; else if (Maxspc <= 50) Numtrial = 10000; else if (Maxspc <= 75) Numtrial = 25000; else Numtrial = 50000; utree_optn = TRUE; /* use first user tree for estimation */ outgroup = 0; /* use first taxon as outgroup */ sym_optn = FALSE; /* symmetrize doublet frequencies */ tstvf84 = 0.0; /* disable F84 model */ show_optn = FALSE; /* show unresolved quartets */ typ_optn = TREERECON_OPTN; /* tree reconstruction */ numclust = 1; /* one clusters in LM analysis */ lmqts = 0; /* all quartets in LM analysis */ compnumqts(); if (Numquartets > 10000) { lmqts = 10000; /* 10000 quartets in LM analysis */ compnumqts(); } /* correct default analysis types if too few/many sequences*/ if ((seqnumcheck!=SEQNUM_OK) && (puzzlemode==QUARTPUZ)) puzzlemode = (puzzlemode + 1) % NUMPUZZLEMODES; /* correct default analysis types if too fewy sequences*/ if ((seqnumcheck==SEQNUM_TOOFEW) && (typ_optn==LIKMAPING_OPTN)) typ_optn = (typ_optn + 1) % NUMTYPES; do { fprintf(STDOUT, "\n\n\nGENERAL OPTIONS"); if (seqnumcheck==SEQNUM_OK) fprintf(STDOUT, "\n"); if (seqnumcheck==SEQNUM_TOOFEW) fprintf(STDOUT, " (no quartet methods available - too few sequences)\n"); if (seqnumcheck==SEQNUM_TOOMANY) fprintf(STDOUT, " (no quartet puzzling available - too many sequences)\n"); fprintf(STDOUT, " b Type of analysis? "); if (typ_optn == TREERECON_OPTN) { if (seqnumcheck==SEQNUM_TOOFEW) fprintf(STDOUT, "Tree reconstruction (only possible)\n"); else fprintf(STDOUT, "Tree reconstruction\n"); } /* not possible for |seqs| < 4 */ if (typ_optn == LIKMAPING_OPTN) fprintf(STDOUT, "Likelihood mapping\n"); if (typ_optn == TREERECON_OPTN) { fprintf(STDOUT, " k Tree search procedure? "); /* not possible for |seqs| < 4 and for |seqs| > 257 */ if (puzzlemode == QUARTPUZ) fprintf(STDOUT, "Quartet puzzling\n"); if (puzzlemode == USERTREE) fprintf(STDOUT, "Evaluate user defined trees\n"); if (puzzlemode == CONSENSUS) fprintf(STDOUT, "Consensus of user defined trees\n"); if (puzzlemode == PAIRDIST) fprintf(STDOUT, "Pairwise distances only (no tree)\n"); if (puzzlemode == QUARTPUZ) { fprintf(STDOUT, " v Approximate quartet likelihood? %s\n", (approxqp ? "Yes" : "No")); fprintf(STDOUT, " u List unresolved quartets? %s\n", (show_optn ? "Yes" : "No")); fprintf(STDOUT, " n Number of puzzling steps? %lu\n", Numtrial); fprintf(STDOUT, " j List puzzling step trees? "); switch (listqptrees) { case PSTOUT_NONE: fprintf(STDOUT, "No\n"); break; case PSTOUT_ORDER: fprintf(STDOUT, "Unique topologies\n"); break; case PSTOUT_LISTORDER: fprintf(STDOUT, "Unique topologies & Chronological list\n"); break; case PSTOUT_LIST: fprintf(STDOUT, "Chronological list only\n"); break; } fprintf(STDOUT, " o Display as outgroup? "); fputid(STDOUT, outgroup); fprintf(STDOUT, " (%d)\n", outgroup + 1); } if (puzzlemode == QUARTPUZ || puzzlemode == USERTREE || puzzlemode == CONSENSUS) { fprintf(STDOUT, " z Compute clocklike branch lengths? "); if (compclock) fprintf(STDOUT, "Yes\n"); else fprintf(STDOUT, "No\n"); } if (compclock) if (puzzlemode == QUARTPUZ || puzzlemode == USERTREE || puzzlemode == CONSENSUS) { fprintf(STDOUT, " l Location of root? "); if (locroot < 0) fprintf(STDOUT, "Best place (automatic search)\n"); else if (locroot < Maxspc) { fprintf(STDOUT, "Branch %d (", locroot + 1); fputid(STDOUT, locroot); fprintf(STDOUT, ")\n"); } else fprintf(STDOUT, "Branch %d (internal branch)\n", locroot + 1); } } if (typ_optn == LIKMAPING_OPTN) { fprintf(STDOUT, " g Group sequences in clusters? "); if (numclust == 1) fprintf(STDOUT, "No\n"); else fprintf(STDOUT, "Yes (%d clusters as specified)\n", numclust); fprintf(STDOUT, " n Number of quartets? "); if (lmqts == 0) fprintf(STDOUT, "%lu (all possible)\n", Numquartets); else fprintf(STDOUT, "%lu (random choice)\n", lmqts); } fprintf(STDOUT, " e Parameter estimates? "); if (approxp_optn) fprintf(STDOUT, "Approximate (faster)\n"); else fprintf(STDOUT, "Exact (slow)\n"); if (!((puzzlemode == USERTREE || puzzlemode == CONSENSUS) && typ_optn == TREERECON_OPTN)) { fprintf(STDOUT, " x Parameter estimation uses? "); if (qcalg_optn) fprintf(STDOUT, "Quartet sampling + NJ tree\n"); else fprintf(STDOUT, "Neighbor-joining tree\n"); } else { fprintf(STDOUT, " x Parameter estimation uses? "); if (utree_optn) fprintf(STDOUT, "1st input tree\n"); else if (qcalg_optn) fprintf(STDOUT, "Quartet sampling + NJ tree\n"); else fprintf(STDOUT, "Neighbor-joining tree\n"); } fprintf(STDOUT, "SUBSTITUTION PROCESS\n"); fprintf(STDOUT, " d Type of sequence input data? "); if (auto_datatype == AUTO_GUESS) fprintf(STDOUT, "Auto: "); if (data_optn == NUCLEOTIDE) fprintf(STDOUT, "Nucleotides\n"); if (data_optn == AMINOACID) fprintf(STDOUT, "Amino acids\n"); if (data_optn == BINARY) fprintf(STDOUT, "Binary states\n"); if (data_optn == NUCLEOTIDE && (Maxseqc % 3) == 0 && !SH_optn) { fprintf(STDOUT, " h Codon positions selected? "); if (codon_optn == 0) fprintf(STDOUT, "Use all positions\n"); if (codon_optn == 1) fprintf(STDOUT, "Use only 1st positions\n"); if (codon_optn == 2) fprintf(STDOUT, "Use only 2nd positions\n"); if (codon_optn == 3) fprintf(STDOUT, "Use only 3rd positions\n"); if (codon_optn == 4) fprintf(STDOUT, "Use 1st and 2nd positions\n"); } fprintf(STDOUT, " m Model of substitution? "); if (data_optn == NUCLEOTIDE) { /* nucleotides */ if (nuc_optn) { if(HKY_optn) fprintf(STDOUT, "HKY (Hasegawa et al. 1985)\n"); if(TN_optn) { fprintf(STDOUT, "TN (Tamura-Nei 1993)\n"); fprintf(STDOUT, " p Constrain TN model to F84 model? "); if (tstvf84 == 0.0) fprintf(STDOUT, "No\n"); else fprintf(STDOUT, "Yes (Ts/Tv ratio = %.2f)\n", tstvf84); } if(GTR_optn) fprintf(STDOUT, "GTR (e.g. Lanave et al. 1980)\n"); if((HKY_optn) || (TN_optn)) { fprintf(STDOUT, " t Transition/transversion parameter? "); if (optim_optn) fprintf(STDOUT, "Estimate from data set\n"); else fprintf(STDOUT, "%.2f\n", TSparam); } if (TN_optn) { fprintf(STDOUT, " r Y/R transition parameter? "); if (optim_optn) fprintf(STDOUT, "Estimate from data set\n"); else fprintf(STDOUT, "%.2f\n", YRparam); } if (GTR_optn) { fprintf(STDOUT, " 1 A-C rate? "); fprintf(STDOUT, "%-23.2f", GTR_ACrate); fprintf(STDOUT, " 2 A-G rate? "); fprintf(STDOUT, "%-23.2f\n", GTR_AGrate); fprintf(STDOUT, " 3 A-T rate? "); fprintf(STDOUT, "%-23.2f", GTR_ATrate); fprintf(STDOUT, " 4 C-G rate? "); fprintf(STDOUT, "%-23.2f\n", GTR_CGrate); fprintf(STDOUT, " 5 C-T rate? "); fprintf(STDOUT, "%-23.2f", GTR_CTrate); fprintf(STDOUT, " 6 G-T rate? "); fprintf(STDOUT, "%-23.2f\n", GTR_GTrate); #if 0 fprintf(STDOUT, " 1 A <-> C mutation rate? "); fprintf(STDOUT, "%.2f\n", GTR_ACrate); fprintf(STDOUT, " 2 A <-> G mutation rate? "); fprintf(STDOUT, "%.2f\n", GTR_AGrate); fprintf(STDOUT, " 3 A <-> T mutation rate? "); fprintf(STDOUT, "%.2f\n", GTR_ATrate); fprintf(STDOUT, " 4 C <-> G mutation rate? "); fprintf(STDOUT, "%.2f\n", GTR_CGrate); fprintf(STDOUT, " 5 C <-> T mutation rate? "); fprintf(STDOUT, "%.2f\n", GTR_CTrate); fprintf(STDOUT, " 6 G <-> T mutation rate? "); fprintf(STDOUT, "%.2f\n", GTR_GTrate); #endif } } if (SH_optn) { fprintf(STDOUT, "SH (Schoeniger-von Haeseler 1994)\n"); fprintf(STDOUT, " t Transition/transversion parameter? "); if (optim_optn) fprintf(STDOUT, "Estimate from data set\n"); else fprintf(STDOUT, "%.2f\n", TSparam); } } if (data_optn == NUCLEOTIDE && SH_optn) { fprintf(STDOUT, " h Doublets defined by? "); if (SHcodon) fprintf(STDOUT, "1st and 2nd codon positions\n"); else fprintf(STDOUT, "1st+2nd, 3rd+4th, etc. site\n"); } if (data_optn == AMINOACID) { /* amino acids */ switch (auto_aamodel) { case AUTO_GUESS: fprintf(STDOUT, "Auto: "); break; case AUTO_DEFAULT: fprintf(STDOUT, "Def.: "); break; } if (Dayhf_optn) fprintf(STDOUT, "Dayhoff (Dayhoff et al. 1978)\n"); if (Jtt_optn) fprintf(STDOUT, "JTT (Jones et al. 1992)\n"); if (mtrev_optn) fprintf(STDOUT, "mtREV24 (Adachi-Hasegawa 1996)\n"); if (cprev_optn) fprintf(STDOUT, "cpREV45 (Adachi et al. 2000)\n"); if (blosum62_optn) fprintf(STDOUT, "BLOSUM62 (Henikoff-Henikoff 92)\n"); if (vtmv_optn) fprintf(STDOUT, "VT (Mueller-Vingron 2000)\n"); if (wag_optn) fprintf(STDOUT, "WAG (Whelan-Goldman 2000)\n"); } if (data_optn == BINARY) { /* binary states */ fprintf(STDOUT, "Two-state model (Felsenstein 1981)\n"); } if (data_optn == AMINOACID) fprintf(STDOUT, " f Amino acid frequencies? "); else if (data_optn == NUCLEOTIDE && SH_optn) fprintf(STDOUT, " f Doublet frequencies? "); else if (data_optn == NUCLEOTIDE && nuc_optn) fprintf(STDOUT, " f Nucleotide frequencies? "); else if (data_optn == BINARY) fprintf(STDOUT, " f Binary state frequencies? "); fprintf(STDOUT, "%s\n", (Frequ_optn ? "Estimate from data set" : "Use specified values")); if (data_optn == NUCLEOTIDE && SH_optn) fprintf(STDOUT, " s Symmetrize doublet frequencies? %s\n", (sym_optn ? "Yes" : "No")); fprintf(STDOUT, "RATE HETEROGENEITY\n"); fprintf(STDOUT, " w Model of rate heterogeneity? "); if (rhetmode == UNIFORMRATE) fprintf(STDOUT, "Uniform rate\n"); if (rhetmode == GAMMARATE ) fprintf(STDOUT, "Gamma distributed rates\n"); if (rhetmode == TWORATE ) fprintf(STDOUT, "Two rates (1 invariable + 1 variable)\n"); if (rhetmode == MIXEDRATE ) fprintf(STDOUT, "Mixed (1 invariable + %d Gamma rates)\n", numcats); if (rhetmode == TWORATE || rhetmode == MIXEDRATE) { fprintf(STDOUT, " i Fraction of invariable sites? "); if (fracinv_optim) fprintf(STDOUT, "Estimate from data set"); else fprintf(STDOUT, "%.2f", fracinv); if (fracinv == 0.0 && !fracinv_optim) fprintf(STDOUT, " (all sites variable)"); fprintf(STDOUT, "\n"); } if (rhetmode == GAMMARATE || rhetmode == MIXEDRATE) { fprintf(STDOUT, " a Gamma distribution parameter alpha? "); if (grate_optim) fprintf(STDOUT, "Estimate from data set\n"); else if (Geta > 0.5) fprintf(STDOUT, "%.2f (strong rate heterogeneity)\n", (1.0-Geta)/Geta); else fprintf(STDOUT, "%.2f (weak rate heterogeneity)\n", (1.0-Geta)/Geta); fprintf(STDOUT, " c Number of Gamma rate categories? %d\n", numcats); } fprintf(STDOUT, "\nQuit [q], confirm [y], or change [menu] settings: "); fflush(STDOUT); /* read one char */ ch = getchar(); if (ch != '\n') { do ; while (getchar() != '\n'); } ch = (char) tolower((int) ch); /* letters in use: a b c d e f g h i j k l m n o p q r s t u v w y x z */ /* letters not in use: */ switch (ch) { case '\n': break; case 'z': if (typ_optn == TREERECON_OPTN && (puzzlemode == QUARTPUZ || puzzlemode == USERTREE || puzzlemode == CONSENSUS)) { compclock = compclock + 1; if (compclock == 2) compclock = 0; } else { fprintf(STDOUT, "\n\n\nThis is not a possible option!\n"); } break; case 'l': if (compclock && typ_optn == TREERECON_OPTN && (puzzlemode == QUARTPUZ || puzzlemode == USERTREE || puzzlemode == CONSENSUS)) { fprintf(STDOUT, "\n\n\nEnter an invalid branch number to search "); fprintf(STDOUT, "for the best location!\n"); fprintf(STDOUT, "\nPlace root at branch (1-%d, 0=automatic): ", 2*Maxspc-3); fflush(STDOUT); scanf("%d", &locroot); do ; while (getchar() != '\n'); if (locroot < 1 || locroot > 2*Maxspc-3) locroot = 0; locroot = locroot - 1; } else { fprintf(STDOUT, "\n\n\nThis is not a possible option!\n"); } break; case 'e': if ((rhetmode == TWORATE || rhetmode == MIXEDRATE) && fracinv_optim) { fprintf(STDOUT, "\n\n\nInvariable sites estimation needs to be exact!\n"); } else { approxp_optn = approxp_optn + 1; if (approxp_optn == 2) approxp_optn = 0; } break; case 'w': rhetmode = rhetmode + 1; if (rhetmode == 4) rhetmode = UNIFORMRATE; if (rhetmode == UNIFORMRATE) { /* uniform rate */ numcats = 1; Geta = 0.05; grate_optim = FALSE; fracinv = 0.0; fracinv_optim = FALSE; } if (rhetmode == GAMMARATE ) { /* Gamma distributed rates */ numcats = 8; Geta = 0.05; grate_optim = TRUE; fracinv = 0.0; fracinv_optim = FALSE; } if (rhetmode == TWORATE ) { /* two rates (1 invariable + 1 variable) */ approxp_optn = FALSE; numcats = 1; Geta = 0.05; grate_optim = FALSE; fracinv = 0.0; fracinv_optim = TRUE; } if (rhetmode == MIXEDRATE ) { /* mixed (1 invariable + Gamma rates) */ approxp_optn = FALSE; numcats = 8; Geta = 0.05; grate_optim = TRUE; fracinv = 0.0; fracinv_optim = TRUE; } break; case 'i': if (rhetmode == TWORATE || rhetmode == MIXEDRATE) { fprintf(STDOUT, "\n\n\nEnter an invalid value for "); fprintf(STDOUT, "estimation from data set!\n"); fprintf(STDOUT, "\nFraction of invariable sites among all sites (%.2f-%.2f): ", MINFI, MAXFI); fflush(STDOUT); scanf("%lf", &fracinv); do ; while (getchar() != '\n'); if (fracinv < MINFI || fracinv > MAXFI) { fracinv_optim = TRUE; fracinv = 0.0; } else { fracinv_optim = FALSE; } } else { fprintf(STDOUT, "\n\n\nThis is not a possible option!\n"); } break; case 'a': if (rhetmode == GAMMARATE || rhetmode == MIXEDRATE) { fprintf(STDOUT, "\n\n\nEnter an invalid value for estimation from data set!\n"); fprintf(STDOUT, "\nGamma distribution parameter alpha (%.2f-%.2f): ", (1.0-MAXGE)/MAXGE, (1.0-MINGE)/MINGE); fflush(STDOUT); scanf("%lf", &Geta); do ; while (getchar() != '\n'); if (Geta < (1.0-MAXGE)/MAXGE || Geta > (1.0-MINGE)/MINGE) { grate_optim = TRUE; Geta = 0.05; } else { grate_optim = FALSE; Geta = 1.0/(1.0 + Geta); } } else fprintf(STDOUT, "\n\n\nThis is not a possible option!\n"); break; case 'c': if (rhetmode == GAMMARATE || rhetmode == MIXEDRATE) { fprintf(STDOUT, "\n\n\nNumber of Gamma rate categories (%d-%d): ", MINCAT, MAXCAT); fflush(STDOUT); scanf("%d", &numcats); do ; while (getchar() != '\n'); if (numcats < MINCAT || numcats > MAXCAT) { fprintf(STDOUT, "\n\n\nThis number of categories is not available!\n"); numcats = 4; } } else { fprintf(STDOUT, "\n\n\nThis is not a possible option!\n"); } break; case 'h': if (data_optn == NUCLEOTIDE && (Maxseqc % 3) == 0 && !SH_optn) { codon_optn = codon_optn + 1; if (codon_optn == 5) codon_optn = 0; translatedataset(Maxspc, Maxseqc, &Maxsite, Seqchars, &Seqchar, &Seqgapchar, &Seqotherchar); /* reestimate nucleotide frequencies only if user did not specify other values */ if (Frequ_optn) estimatebasefreqs(); } else if (data_optn == NUCLEOTIDE && SH_optn) { if (Maxseqc % 2 != 0 && Maxseqc % 3 == 0) { SHcodon = TRUE; fprintf(STDOUT, "\n\n\nThis is the only possible option for the data set!\n"); } if (Maxseqc % 3 != 0 && Maxseqc % 2 == 0) { SHcodon = FALSE; fprintf(STDOUT, "\n\n\nThis is the only possible option for the data set!\n"); } if (Maxseqc % 2 == 0 && Maxseqc % 3 == 0) { if (SHcodon) SHcodon = FALSE; else SHcodon = TRUE; translatedataset(Maxspc, Maxseqc, &Maxsite, Seqchars, &Seqchar, &Seqgapchar, &Seqotherchar); /* reestimate nucleotide frequencies only if user did not specify other values */ if (Frequ_optn) estimatebasefreqs(); } } else { fprintf(STDOUT, "\n\n\nThis is not a possible option!\n"); } break; case 'x': if (typ_optn == TREERECON_OPTN && (puzzlemode == USERTREE || puzzlemode == CONSENSUS)) { /* use of usertree for parameter estimation set? */ /* utree_optn==TRUE && qcalg_optn==? - 1st user tree (for substitution process and rate variation) */ /* utree_optn==FALSE && qcalg_optn==TRUE - quartet sampling (for substitution process) + NJ tree (for rate variation) */ /* utree_optn==FALSE && qcalg_optn==FALSE - neighbor-joining tree (for substitution process and rate variation) */ if (utree_optn) { /* menu point 1 (1st utree) -> 2 (NJ) */ utree_optn = FALSE; /* no 1st usertree */ qcalg_optn = FALSE; /* no quartets */ } else { /* menu point 2 (NJ) -> 3 (NJ+Q) */ qcalg_optn = qcalg_optn + 1; /* seq-num < 4: only 1' (NJ) possible */ if ((seqnumcheck==SEQNUM_TOOFEW) && (qcalg_optn==1)) qcalg_optn = qcalg_optn + 1; if (qcalg_optn == 2) { /* menu point 3 (NJ+Q) -> 1 (1st utree) */ qcalg_optn = 0; utree_optn = TRUE; } } } else { /* menu point 1' (NJ) -> 2' (NJ+Q) */ qcalg_optn = qcalg_optn + 1; /* menu point 2' (NJ+Q) -> 1' (NJ) */ if (qcalg_optn == 2) qcalg_optn = 0; /* seq-num < 4: only 1' (NJ) possible */ if ((seqnumcheck==SEQNUM_TOOFEW) && (qcalg_optn==1)) qcalg_optn=0; } break; case 'k': if (typ_optn == TREERECON_OPTN) { puzzlemode = (puzzlemode + 1) % NUMPUZZLEMODES; if ((seqnumcheck!=SEQNUM_OK) && (puzzlemode==QUARTPUZ)) puzzlemode = (puzzlemode + 1) % NUMPUZZLEMODES; } else { fprintf(STDOUT, "\n\n\nThis is not a possible option!\n"); } break; case 'b': typ_optn = (typ_optn + 1) % NUMTYPES; if ((seqnumcheck==SEQNUM_TOOFEW) && (typ_optn==LIKMAPING_OPTN)) typ_optn = (typ_optn + 1) % NUMTYPES; break; case 'g': if (typ_optn == LIKMAPING_OPTN) { clustA = clustB = clustC = clustD = 0; if (numclust != 1) { numclust = 1; } else { fprintf(STDOUT, "\n\n\nNumber of clusters (2-4): "); fflush(STDOUT); scanf("%d", &numclust); do ; while (getchar() != '\n'); if (numclust < 2 || numclust > 4) { numclust = 1; fprintf(STDOUT, "\n\n\nOnly 2, 3, or 4 "); fprintf(STDOUT, "clusters possible\n"); } else { fprintf(STDOUT, "\nDistribute all sequences over the "); if (numclust == 2) { fprintf(STDOUT, "two clusters a and b (At least two\n"); fprintf(STDOUT, "sequences per cluster are necessary), "); } if (numclust == 3) { fprintf(STDOUT, "three clusters a, b, and c\n"); fprintf(STDOUT, "(At least one sequence in cluster a and b, and at least two\n"); fprintf(STDOUT, "sequences in c are necessary), "); } if (numclust == 4) { fprintf(STDOUT, "four clusters a, b, c, and d\n"); fprintf(STDOUT, "(At least one sequence per cluster is necessary),\n"); } fprintf(STDOUT, "type x to exclude a sequence:\n\n"); for (i = 0; i < Maxspc; i++) { valid = FALSE; do { fputid10(STDOUT, i); fprintf(STDOUT, ": "); fflush(STDOUT); /* read one char */ ch = getchar(); if (ch != '\n') { do ; while (getchar() != '\n'); } ch = (char) tolower((int) ch); if (ch == 'a' || ch == 'b' || ch == 'x') valid = TRUE; if (numclust == 3 || numclust == 4) if (ch == 'c') valid = TRUE; if (numclust == 4) if (ch == 'd') valid = TRUE; } while (!valid); if (ch == 'a') { clusterA[clustA] = i; clustA++; } if (ch == 'b') { clusterB[clustB] = i; clustB++; } if (ch == 'c') { clusterC[clustC] = i; clustC++; } if (ch == 'd') { clusterD[clustD] = i; clustD++; } } /* check clusters */ valid = TRUE; if (numclust == 4) { if (clustA == 0) { valid = FALSE; numclust = 1; fprintf(STDOUT, "\n\n\nNo sequence in cluster a\n"); } if (clustB == 0) { valid = FALSE; numclust = 1; fprintf(STDOUT, "\n\n\nNo sequence in cluster b\n"); } if (clustC == 0) { valid = FALSE; numclust = 1; fprintf(STDOUT, "\n\n\nNo sequence in cluster c\n"); } if (clustD == 0) { valid = FALSE; numclust = 1; fprintf(STDOUT, "\n\n\nNo sequence in cluster d\n"); } } if (numclust == 3) { if (clustA == 0) { valid = FALSE; numclust = 1; fprintf(STDOUT, "\n\n\nNo sequence in cluster a\n"); } if (clustB == 0) { valid = FALSE; numclust = 1; fprintf(STDOUT, "\n\n\nNo sequence in cluster b\n"); } if (clustC < 2) { valid = FALSE; numclust = 1; if (clustC == 0) fprintf(STDOUT, "\n\n\nNo sequence in cluster c\n"); else fprintf(STDOUT, "\n\n\nOnly one sequence in cluster c\n"); } } if (numclust == 2) { if (clustA < 2) { valid = FALSE; numclust = 1; if (clustA == 0) fprintf(STDOUT, "\n\n\nNo sequence in cluster a\n"); else fprintf(STDOUT, "\n\n\nOnly one sequence in cluster a\n"); } if (clustB < 2) { valid = FALSE; numclust = 1; if (clustB == 0) fprintf(STDOUT, "\n\n\nNo sequence in cluster b\n"); else fprintf(STDOUT, "\n\n\nOnly one sequence in cluster b\n"); } } if (valid) { fprintf(STDOUT, "\nNumber of sequences in each cluster:\n\n"); fprintf(STDOUT, "Cluster a: %d\n", clustA); fprintf(STDOUT, "Cluster b: %d\n", clustB); if (numclust > 2) fprintf(STDOUT, "Cluster c: %d\n", clustC); if (numclust == 4) fprintf(STDOUT, "Cluster d: %d\n", clustD); fprintf(STDOUT, "\nExcluded sequences: "); if (numclust == 2) fprintf(STDOUT, "%d\n", Maxspc-clustA-clustB); if (numclust == 3) fprintf(STDOUT, "%d\n", Maxspc-clustA-clustB-clustC); if (numclust == 4) fprintf(STDOUT, "%d\n", Maxspc-clustA-clustB-clustC-clustD); } } } /* number of resulting quartets */ compnumqts(); } else { fprintf(STDOUT, "\n\n\nThis is not a possible option!\n"); } break; case 'd': if (auto_datatype == AUTO_GUESS) { auto_datatype = AUTO_OFF; guessdata_optn = data_optn; data_optn = 0; } else { data_optn = data_optn + 1; if (data_optn == 3) { auto_datatype = AUTO_GUESS; data_optn = guessdata_optn; } } /* translate characters into format used by ML engine */ translatedataset(Maxspc, Maxseqc, &Maxsite, Seqchars, &Seqchar, &Seqgapchar, &Seqotherchar); estimatebasefreqs(); break; case 'u': if (puzzlemode == QUARTPUZ && typ_optn == TREERECON_OPTN) show_optn = 1 - show_optn; else fprintf(STDOUT, "\n\n\nThis is not a possible option!\n"); break; case 'j': if (puzzlemode == QUARTPUZ && typ_optn == TREERECON_OPTN) listqptrees = (listqptrees + 1) % 4; else fprintf(STDOUT, "\n\n\nThis is not a possible option!\n"); break; case 'v': if (puzzlemode == QUARTPUZ && typ_optn == TREERECON_OPTN) approxqp = 1 - approxqp; else fprintf(STDOUT, "\n\n\nThis is not a possible option!\n"); break; case 'f': if (Frequ_optn) { tstvf84 = 0.0; Frequ_optn = FALSE; sumfreq = 0.0; if (data_optn == AMINOACID) fprintf(STDOUT, "\n\n\nAmino acid"); else if (data_optn == NUCLEOTIDE && SH_optn) fprintf(STDOUT, "\n\n\nDoublet"); else if (data_optn == NUCLEOTIDE && nuc_optn) fprintf(STDOUT, "\n\n\nNucleotide"); else if (data_optn == BINARY) fprintf(STDOUT, "\n\n\nBinary state"); fprintf(STDOUT, " frequencies (in %%):\n\n"); for (i = 0; i < gettpmradix() - 1; i++) { fprintf(STDOUT, "pi(%s) = ", int2code(i)); fflush(STDOUT); scanf("%lf", &(Freqtpm[i])); do ; while (getchar() != '\n'); Freqtpm[i] = Freqtpm[i]/100.0; if (Freqtpm[i] < 0.0) { fprintf(STDOUT, "\n\n\nNegative frequency not possible\n"); estimatebasefreqs(); break; } sumfreq = sumfreq + Freqtpm[i]; if (sumfreq > 1.0) { fprintf(STDOUT, "\n\n\nThe sum of "); fprintf(STDOUT, "all frequencies exceeds"); fprintf(STDOUT, " 100%%\n"); estimatebasefreqs(); break; } if (i == gettpmradix() - 2) Freqtpm[i+1] = 1.0 - sumfreq; } } else estimatebasefreqs(); break; case 's': if (data_optn == NUCLEOTIDE && SH_optn) { sym_optn = 1 - sym_optn; } else { fprintf(STDOUT, "\n\n\nThis is not a possible option!\n"); } break; case 'n': if (puzzlemode == QUARTPUZ && typ_optn == TREERECON_OPTN) { fprintf(STDOUT, "\n\n\nNumber of puzzling steps: "); fflush(STDOUT); scanf("%lu", &Numtrial); do ; while (getchar() != '\n'); if (Numtrial < 1) { fprintf(STDOUT, "\n\n\nThe number of puzzling"); fprintf(STDOUT, " steps can't be smaller than one\n"); Numtrial = 1000; } } else if (typ_optn == LIKMAPING_OPTN) { fprintf(STDOUT, "\n\nEnter zero to use all possible"); fprintf(STDOUT, " quartets in the analysis!\n"); fprintf(STDOUT, "\nNumber of random quartets: "); fflush(STDOUT); scanf("%lu", &lmqts); do ; while (getchar() != '\n'); /* compute number of quartets used */ compnumqts(); } else { fprintf(STDOUT, "\n\n\nThis is not a possible option!\n"); } break; case 'o': if (puzzlemode == QUARTPUZ && typ_optn == TREERECON_OPTN) { fprintf(STDOUT, "\n\n\nSequence to be displayed as outgroup (1-%d, or 0 for last): ", Maxspc); fflush(STDOUT); scanf("%d", &outgroup); do ; while (getchar() != '\n'); if (outgroup < 0 || outgroup > Maxspc) { fprintf(STDOUT, "\n\n\nSequences are numbered "); fprintf(STDOUT, "from 1 to %d\n", Maxspc); outgroup = 1; } if (outgroup == 0) outgroup = Maxspc; outgroup = outgroup - 1; } else { fprintf(STDOUT, "\n\n\nThis is not a possible option!\n"); } break; case 'm': if (data_optn == NUCLEOTIDE) { /* nucleotide data */ #ifndef USE_GTR if(HKY_optn && nuc_optn) { /* HKY -> TN */ tstvf84 = 0.0; TSparam = 2.0; YRparam = 0.9; HKY_optn = FALSE; TN_optn = TRUE; GTR_optn = FALSE; optim_optn = TRUE; nuc_optn = TRUE; SH_optn = FALSE; break; } #else if(HKY_optn && nuc_optn) { /* HKY -> TN */ tstvf84 = 0.0; TSparam = 2.0; YRparam = 0.9; HKY_optn = FALSE; TN_optn = TRUE; GTR_optn = FALSE; optim_optn = TRUE; nuc_optn = TRUE; SH_optn = FALSE; break; } if(TN_optn && nuc_optn) { /* TN -> GTR */ tstvf84 = 0.0; TSparam = 2.0; YRparam = 0.9; GTR_ACrate = 1.0; GTR_AGrate = 1.0; GTR_ATrate = 1.0; GTR_CGrate = 1.0; GTR_CTrate = 1.0; GTR_GTrate = 1.0; HKY_optn = FALSE; TN_optn = FALSE; GTR_optn = TRUE; optim_optn = FALSE; nuc_optn = TRUE; SH_optn = FALSE; break; } #if 0 if(GTR_optn && nuc_optn) { /* GTR -> TN */ tstvf84 = 0.0; TSparam = 2.0; YRparam = 0.9; HKY_optn = FALSE; TN_optn = TRUE; GTR_optn = FALSE; optim_optn = TRUE; nuc_optn = TRUE; SH_optn = FALSE; break; } #endif #endif if(GTR_optn && nuc_optn) { /* if(TN_optn && nuc_optn) { */ if (Maxseqc % 2 == 0 || Maxseqc % 3 == 0) { /* number of chars needs to be a multiple 2 or 3 */ /* TN -> SH */ if (Maxseqc % 2 != 0 && Maxseqc % 3 == 0) SHcodon = TRUE; else SHcodon = FALSE; tstvf84 = 0.0; TSparam = 2.0; YRparam = 1.0; HKY_optn = TRUE; TN_optn = FALSE; GTR_optn = FALSE; optim_optn = TRUE; nuc_optn = FALSE; SH_optn = TRUE; /* translate characters into format */ /* used by ML engine */ translatedataset(Maxspc, Maxseqc, &Maxsite, Seqchars, &Seqchar, &Seqgapchar, &Seqotherchar); estimatebasefreqs(); } else { fprintf(STDOUT, "\n\n\nSH model not "); fprintf(STDOUT, "available for the data set!\n"); /* TN -> HKY */ tstvf84 = 0.0; TSparam = 2.0; YRparam = 1.0; HKY_optn = TRUE; TN_optn = FALSE; GTR_optn = FALSE; optim_optn = TRUE; nuc_optn = TRUE; SH_optn = FALSE; } break; } if(SH_optn) { /* SH -> HKY */ tstvf84 = 0.0; TSparam = 2.0; YRparam = 1.0; HKY_optn = TRUE; TN_optn = FALSE; GTR_optn = FALSE; optim_optn = TRUE; nuc_optn = TRUE; SH_optn = FALSE; /* translate characters into format */ /* used by ML engine */ translatedataset(Maxspc, Maxseqc, &Maxsite, Seqchars, &Seqchar, &Seqgapchar, &Seqotherchar); estimatebasefreqs(); break; } break; } if (data_optn == AMINOACID) { /* amino acid data */ if (auto_aamodel) { /* AUTO -> Dayhoff */ Dayhf_optn = TRUE; Jtt_optn = FALSE; mtrev_optn = FALSE; cprev_optn = FALSE; blosum62_optn = FALSE; vtmv_optn = FALSE; wag_optn = FALSE; auto_aamodel = AUTO_OFF; break; } if (Dayhf_optn) { /* Dayhoff -> JTT */ Dayhf_optn = FALSE; Jtt_optn = TRUE; mtrev_optn = FALSE; cprev_optn = FALSE; blosum62_optn = FALSE; vtmv_optn = FALSE; wag_optn = FALSE; auto_aamodel = AUTO_OFF; break; } if (Jtt_optn) { /* JTT -> mtREV */ Dayhf_optn = FALSE; Jtt_optn = FALSE; mtrev_optn = TRUE; cprev_optn = FALSE; blosum62_optn = FALSE; vtmv_optn = FALSE; wag_optn = FALSE; auto_aamodel = AUTO_OFF; break; } #ifdef CPREV if (mtrev_optn) { /* mtREV -> cpREV */ Dayhf_optn = FALSE; Jtt_optn = FALSE; mtrev_optn = FALSE; cprev_optn = TRUE; blosum62_optn = FALSE; vtmv_optn = FALSE; wag_optn = FALSE; auto_aamodel = AUTO_OFF; break; } #else /* ! CPREV */ if (mtrev_optn) { /* mtREV -> BLOSUM 62 */ Dayhf_optn = FALSE; Jtt_optn = FALSE; mtrev_optn = FALSE; cprev_optn = FALSE; blosum62_optn = TRUE; vtmv_optn = FALSE; wag_optn = FALSE; auto_aamodel = AUTO_OFF; break; } #endif /* ! CPREV */ #ifdef CPREV if (cprev_optn) { /* cpREV -> BLOSUM 62 */ Dayhf_optn = FALSE; Jtt_optn = FALSE; mtrev_optn = FALSE; cprev_optn = FALSE; blosum62_optn = TRUE; vtmv_optn = FALSE; wag_optn = FALSE; auto_aamodel = AUTO_OFF; break; } #endif if (blosum62_optn) { /* BLOSUM 62 -> VT model */ Dayhf_optn = FALSE; Jtt_optn = FALSE; mtrev_optn = FALSE; cprev_optn = FALSE; blosum62_optn = FALSE; vtmv_optn = TRUE; wag_optn = FALSE; auto_aamodel = AUTO_OFF; break; } if (vtmv_optn) { /* VT model -> WAG model */ Dayhf_optn = FALSE; Jtt_optn = FALSE; mtrev_optn = FALSE; cprev_optn = FALSE; blosum62_optn = FALSE; vtmv_optn = FALSE; wag_optn = TRUE; auto_aamodel = AUTO_OFF; break; } if (wag_optn) { /* WAG model -> AUTO */ Dayhf_optn = guessDayhf_optn; Jtt_optn = guessJtt_optn; mtrev_optn = guessmtrev_optn; cprev_optn = guesscprev_optn; blosum62_optn = guessblosum62_optn; vtmv_optn = guessvtmv_optn; wag_optn = guesswag_optn; auto_aamodel = guessauto_aamodel; break; } break; } if (data_optn == BINARY) { fprintf(STDOUT, "\n\n\nNo other model available!\n"); } break; case 't': if (data_optn != NUCLEOTIDE) { fprintf(STDOUT, "\n\n\nThis is not a possible option!\n"); } else { tstvf84 = 0.0; fprintf(STDOUT, "\n\n\nEnter an invalid value for "); fprintf(STDOUT, "estimation from data set!\n"); fprintf(STDOUT, "\nTransition/transversion parameter (%.2f-%.2f): ", MINTS, MAXTS); fflush(STDOUT); scanf("%lf", &TSparam); do ; while (getchar() != '\n'); if (TSparam < MINTS || TSparam > MAXTS) { optim_optn = TRUE; TSparam = 2.0; } else { optim_optn = FALSE; } } break; case 'q': fprintf(STDOUT, "\n\n\n"); # if PARALLEL PP_SendDone(); MPI_Finalize(); # endif /* PARALLEL */ exit(0); break; case 'r': if (!(TN_optn && nuc_optn)){ fprintf(STDOUT, "\n\n\nThis is not a possible option!\n"); } else { tstvf84 = 0.0; fprintf(STDOUT, "\n\n\nEnter an invalid value "); fprintf(STDOUT, "for estimation from data set!\n"); fprintf(STDOUT, "\nY/R transition parameter (%.2f-%.2f): ", MINYR, MAXYR); fflush(STDOUT); scanf("%lf", &YRparam); do ; while (getchar() != '\n'); if (YRparam < MINYR || YRparam > MAXYR) { optim_optn = TRUE; YRparam = 0.9; } else if (YRparam == 1.0) { TN_optn = FALSE; HKY_optn = TRUE; if (optim_optn) TSparam = 2.0; } else { optim_optn = FALSE; } } break; case 'p': if (!(TN_optn && nuc_optn)){ fprintf(STDOUT, "\n\n\nThis is not a possible option!\n"); } else { fprintf(STDOUT, "\n\n\nThe F84 model (Felsenstein 1984) is a restricted"); fprintf(STDOUT, " TN model, and the one\nF84 parameter uniquely"); fprintf(STDOUT, " determines the two corresponding TN parameters!\n\n"); fprintf(STDOUT, "F84 expected transition/transversion ratio: "); fflush(STDOUT); scanf("%lf", &tstvf84); do ; while (getchar() != '\n'); if (tstvf84 <= 0.0) tstvf84 = 0.0; else makeF84model(); } break; case '1': if (!(GTR_optn && nuc_optn)){ fprintf(STDOUT, "\n\n\nThis is not a possible option!\n"); } else { fprintf(STDOUT, "\nA-C substitution rate: "); fflush(STDOUT); scanf("%lf", >R_ACrate); do ; while (getchar() != '\n'); } break; case '2': if (!(GTR_optn && nuc_optn)){ fprintf(STDOUT, "\n\n\nThis is not a possible option!\n"); } else { fprintf(STDOUT, "\nA-G substitution rate: "); fflush(STDOUT); scanf("%lf", >R_AGrate); do ; while (getchar() != '\n'); } break; case '3': if (!(GTR_optn && nuc_optn)){ fprintf(STDOUT, "\n\n\nThis is not a possible option!\n"); } else { fprintf(STDOUT, "\nA-T substitution rate: "); fflush(STDOUT); scanf("%lf", >R_ATrate); do ; while (getchar() != '\n'); } break; case '4': if (!(GTR_optn && nuc_optn)){ fprintf(STDOUT, "\n\n\nThis is not a possible option!\n"); } else { fprintf(STDOUT, "\nC-G substitution rate: "); fflush(STDOUT); scanf("%lf", >R_CGrate); do ; while (getchar() != '\n'); } break; case '5': if (!(GTR_optn && nuc_optn)){ fprintf(STDOUT, "\n\n\nThis is not a possible option!\n"); } else { fprintf(STDOUT, "\nC-T substitution rate: "); fflush(STDOUT); scanf("%lf", >R_CTrate); do ; while (getchar() != '\n'); } break; case '6': if (!(GTR_optn && nuc_optn)){ fprintf(STDOUT, "\n\n\nThis is not a possible option!\n"); } else { fprintf(STDOUT, "\nG-T substitution rate: "); fflush(STDOUT); scanf("%lf", >R_GTrate); do ; while (getchar() != '\n'); } break; case 'y': fprintf(STDOUT, "\n"); break; default: fprintf(STDOUT, "\n\n\nThis is not a possible option!\n"); break; } } while (ch != 'y'); { int gaperror = 0; int notu; for (notu = 0; notu < Maxspc; notu++) { #ifndef USE_WINDOWS if ((Seqgapchar[notu] + Seqotherchar[notu]) == Maxsite) { #else if ((Seqgapchar[notu] + Seqotherchar[notu]) == alimaxsite) { #endif if (gaperror == 0) { fprintf(STDOUT, "\n\n\n"); fprintf(STDOUT, "\n\n\nUnable to proceed (only ambiguous characters ('-', '?', 'X', ...) \nin sequence(s) '"); } else { fprintf(STDOUT, "', '"); } fputid(STDOUT, notu); gaperror++; } if (gaperror > 0) { fprintf(STDOUT, "')\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } } /* for */ } } /* setoptions */ /* open file for reading */ int openfiletoread(FILE **fp, char name[], char descr[]) { int count = 0; int reset = 0; cvector str; if ((*fp = fopen(name, "r")) == NULL) { fprintf(STDOUT, "\n\n\nPlease enter a file name for the %s: ", descr); fflush(STDOUT); str = mygets(); while ((*fp = fopen(str, "r")) == NULL) { count++; if (count > 10) { fprintf(STDOUT, "\n\n\nToo many trials - quitting ...\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } fprintf(STDOUT, "File '%s' not found, ", str); fprintf(STDOUT, "please enter alternative name: "); free_cvector(str); fflush(STDOUT); str = mygets(); reset = 1; } fprintf(STDOUT, "\n"); strcpy(name, str); free_cvector(str); } return(reset); } /* openfiletoread */ /* open file for writing */ int openfiletowrite(FILE **fp, char name[], char descr[]) { int count = 0; int reset = 0; cvector str; if ((*fp = fopen(name, "w")) == NULL) { fprintf(STDOUT, "\n\n\nPlease enter a file name for the %s: ", descr); fflush(STDOUT); str = mygets(); while ((*fp = fopen(str, "w")) == NULL) { count++; if (count > 10) { fprintf(STDOUT, "\n\n\nToo many trials - quitting ...\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } fprintf(STDOUT, "File '%s' not created, ", str); fprintf(STDOUT, "please enter other name: "); free_cvector(str); fflush(STDOUT); str = mygets(); reset = 1; } fprintf(STDOUT, "\n"); strcpy(name, str); free_cvector(str); } return(reset); } /* openfiletowrite */ /* open file for appending */ int openfiletoappend(FILE **fp, char name[], char descr[]) { int count = 0; int reset = 0; cvector str; if ((*fp = fopen(name, "a")) == NULL) { fprintf(STDOUT, "\n\n\nPlease enter a file name for the %s: ", descr); fflush(STDOUT); str = mygets(); while ((*fp = fopen(str, "a")) == NULL) { count++; if (count > 10) { fprintf(STDOUT, "\n\n\nToo many trials - quitting ...\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } fprintf(STDOUT, "File '%s' not created, ", str); fprintf(STDOUT, "please enter other name: "); free_cvector(str); fflush(STDOUT); str = mygets(); reset = 1; } fprintf(STDOUT, "\n"); strcpy(name, str); free_cvector(str); } return(reset); } /* openfiletoappend */ /* close file */ void closefile(FILE *fp) { fclose(fp); } /* closefile */ /* symmetrize doublet frequencies */ void symdoublets() { int i, imean; double mean; if (data_optn == NUCLEOTIDE && SH_optn && sym_optn) { /* ML frequencies */ mean = (Freqtpm[1] + Freqtpm[4])/2.0; /* AC CA */ Freqtpm[1] = mean; Freqtpm[4] = mean; mean = (Freqtpm[2] + Freqtpm[8])/2.0; /* AG GA */ Freqtpm[2] = mean; Freqtpm[8] = mean; mean = (Freqtpm[3] + Freqtpm[12])/2.0; /* AT TA */ Freqtpm[3] = mean; Freqtpm[12] = mean; mean = (Freqtpm[6] + Freqtpm[9])/2.0; /* CG GC */ Freqtpm[6] = mean; Freqtpm[9] = mean; mean = (Freqtpm[7] + Freqtpm[13])/2.0; /* CT TC */ Freqtpm[7] = mean; Freqtpm[13] = mean; mean = (Freqtpm[11] + Freqtpm[14])/2.0; /* GT TG */ Freqtpm[11] = mean; Freqtpm[14] = mean; /* base composition of each taxon */ for (i = 0; i < Maxspc; i++) { imean = (Basecomp[i][1] + Basecomp[i][4])/2; /* AC CA */ Basecomp[i][1] = imean; Basecomp[i][4] = imean; imean = (Basecomp[i][2] + Basecomp[i][8])/2; /* AG GA */ Basecomp[i][2] = imean; Basecomp[i][8] = imean; imean = (Basecomp[i][3] + Basecomp[i][12])/2; /* AT TA */ Basecomp[i][3] = imean; Basecomp[i][12] = imean; imean = (Basecomp[i][6] + Basecomp[i][9])/2; /* CG GC */ Basecomp[i][6] = imean; Basecomp[i][9] = imean; imean = (Basecomp[i][7] + Basecomp[i][13])/2; /* CT TC */ Basecomp[i][7] = imean; Basecomp[i][13] = imean; imean = (Basecomp[i][11] + Basecomp[i][14])/2; /* GT TG */ Basecomp[i][11] = imean; Basecomp[i][14] = imean; } } } /* symdoublets */ /* show Ts/Tv ratio and Ts Y/R ratio */ void computeexpectations() { double AlphaYBeta, AlphaRBeta, piR, piY, num, denom, pyr, pur; if (nuc_optn == TRUE) { /* 4x4 nucs */ piR = Freqtpm[0] + Freqtpm[2]; piY = Freqtpm[1] + Freqtpm[3]; AlphaRBeta = 4.0*TSparam / (1 + YRparam); AlphaYBeta = AlphaRBeta * YRparam; tstvratio = (AlphaRBeta*Freqtpm[0]*Freqtpm[2] + AlphaYBeta*Freqtpm[1]*Freqtpm[3])/(piR * piY); yrtsratio = (AlphaYBeta*Freqtpm[1]*Freqtpm[3]) / (AlphaRBeta*Freqtpm[0]*Freqtpm[2]); } else { /* 16x16 nucs */ pyr = Freqtpm[1]*Freqtpm[3] + Freqtpm[5]*Freqtpm[7] + Freqtpm[9]*Freqtpm[11] + Freqtpm[4]*Freqtpm[12] + Freqtpm[5]*Freqtpm[13] + Freqtpm[6]*Freqtpm[14] + Freqtpm[7]*Freqtpm[15] + Freqtpm[13]*Freqtpm[15]; pur = Freqtpm[0]*Freqtpm[2] + Freqtpm[4]*Freqtpm[6] + Freqtpm[0]*Freqtpm[8] + Freqtpm[1]*Freqtpm[9] + Freqtpm[2]*Freqtpm[10] + Freqtpm[8]*Freqtpm[10] + Freqtpm[3]*Freqtpm[11] + Freqtpm[12]*Freqtpm[14]; num = pyr + pur; denom = Freqtpm[0]*Freqtpm[1] + Freqtpm[1]*Freqtpm[2] + Freqtpm[0]*Freqtpm[3] + Freqtpm[2]*Freqtpm[3] + Freqtpm[0]*Freqtpm[4] + Freqtpm[1]*Freqtpm[5] + Freqtpm[4]*Freqtpm[5] + Freqtpm[2]*Freqtpm[6] + Freqtpm[5]*Freqtpm[6] + Freqtpm[3]*Freqtpm[7] + Freqtpm[4]*Freqtpm[7] + Freqtpm[6]*Freqtpm[7] + Freqtpm[4]*Freqtpm[8] + Freqtpm[5]*Freqtpm[9] + Freqtpm[8]*Freqtpm[9] + Freqtpm[6]*Freqtpm[10] + Freqtpm[9]*Freqtpm[10] + Freqtpm[7]*Freqtpm[11] + Freqtpm[8]*Freqtpm[11] + Freqtpm[10]*Freqtpm[11] + Freqtpm[0]*Freqtpm[12] + Freqtpm[8]*Freqtpm[12] + Freqtpm[1]*Freqtpm[13] + Freqtpm[9]*Freqtpm[13] + Freqtpm[12]*Freqtpm[13] + Freqtpm[2]*Freqtpm[14] + Freqtpm[10]*Freqtpm[14] + Freqtpm[13]*Freqtpm[14] + Freqtpm[3]*Freqtpm[15] + Freqtpm[11]*Freqtpm[15] + Freqtpm[12]*Freqtpm[15] + Freqtpm[14]*Freqtpm[15]; tstvratio = 2.0*TSparam * num/denom; yrtsratio = pyr/pur; } } /* computeexpectations */ /* write ML distance matrix to file */ void putdistance(FILE *fp) { int i, j; fprintf(fp, " %d\n", Maxspc); for (i = 0; i < Maxspc; i++) { fputid10(fp, i); for (j = 0; j < Maxspc; j++) { fprintf(fp, " %.5f", Distanmat[i][j]/100.0); /* seven in one row */ if ((j + 1) % 7 == 0 && j+1 != Maxspc) fprintf(fp, "\n "); } fprintf(fp, "\n"); } } /* putdistance */ /* find identical sequences */ void findidenticals(FILE *fp) { int i, j, noids; cvector useqs; useqs = new_cvector(Maxspc); for (i = 0; i < Maxspc; i++) useqs[i] = 0; noids = TRUE; for (i = 0; i < Maxspc && noids; i++) for (j = i + 1; j < Maxspc && noids; j++) if (Distanmat[i][j] == 0.0) noids = FALSE; if (noids) fprintf(fp, " All sequences are unique.\n"); else { for (i = 0; i < Maxspc; i++) { noids = TRUE; for (j = i + 1; j < Maxspc && noids; j++) if (Distanmat[i][j] == 0.0) noids = FALSE; if (!noids && useqs[i] == 0) { fputid(fp, i); useqs[i] = 1; for (j = i + 1; j < Maxspc; j++) if (Distanmat[i][j] == 0.0) { fprintf(fp, ", "); fputid(fp, j); useqs[j] = 1; } fprintf(fp, ".\n"); } } } free_cvector(useqs); } /* findidenticals */ /* compute average distance */ double averagedist(int maxspc, dmatrix distanmat, double *meandist, double *mindist, double *maxdist, double *stddevdist, double *vardist) { int i, j; double sum; double avg; double min; double max; double var; double stddev; double temp; double numofdists; numofdists = ((double) (maxspc * (maxspc - 1)) / 2.0); sum = 0.0; for (i = 0; i < maxspc; i++) for (j = i + 1; j < maxspc; j++) sum = sum + distanmat[i][j]; /* avg = sum / (double) maxspc / ((double) maxspc - 1.0) * 2.0; */ /* avg = sum / ((double) (maxspc * (maxspc - 1)) / 2.0); */ avg = sum / numofdists; /* fprintf(stderr, "\nXXXX: old %f, new %f\n", 1 / (double) maxspc / ((double) maxspc - 1.0) * 2.0, 1 / ((double) (maxspc * (maxspc - 1)) / 2.0)); */ sum = 0.0; min = distanmat[0][1]; max = distanmat[0][1]; for (i = 0; i < maxspc; i++) for (j = i + 1; j < maxspc; j++) { temp = avg/100 - distanmat[i][j]/100; sum += temp * temp; if (min > distanmat[i][j]) min = distanmat[i][j]; if (max < distanmat[i][j]) max = distanmat[i][j]; } var = sum / (numofdists - 1); stddev = sqrt(var); #if 0 fprintf(stderr, "\nXXXX: mean=%f, min=%f max=%f variance=%f, std-deviation=%f\n", avg/100, min/100, max/100, var, stddev); #endif *meandist = avg/100; *mindist = min/100; *maxdist = max/100; *vardist = var; *stddevdist = stddev; return avg; } /* averagedist */ /* first lines of EPSF likelihood mapping file */ void initps(FILE *ofp) { fprintf(ofp, "%%!PS-Adobe-3.0 EPSF-3.0\n"); fprintf(ofp, "%%%%BoundingBox: 60 210 550 650\n"); fprintf(ofp, "%%%%Pages: 1\n"); # ifndef ALPHA fprintf(ofp, "%%%%Creator: %s (version %s)\n", PACKAGE, VERSION); # else fprintf(ofp, "%%%%Creator: %s (version %s%s)\n", PACKAGE, VERSION, ALPHA); # endif fprintf(ofp, "%%%%Title: Likelihood Mapping Analysis\n"); fprintf(ofp, "%%%%CreationDate: %s", asctime(localtime(&Starttime)) ); fprintf(ofp, "%%%%DocumentFonts: Helvetica\n"); fprintf(ofp, "%%%%DocumentNeededFonts: Helvetica\n"); fprintf(ofp, "%%%%EndComments\n"); fprintf(ofp, "%% use inch as unit\n"); fprintf(ofp, "/inch {72 mul} def\n"); fprintf(ofp, "%% triangle side length (3 inch)\n"); fprintf(ofp, "/tl {3 inch mul} def\n"); fprintf(ofp, "%% plot one dot (x-y coordinates on stack)\n"); fprintf(ofp, "/dot {\n"); fprintf(ofp, "newpath\n"); fprintf(ofp, "0.002 tl 0 360 arc %% radius is 0.002 of the triangle length\n"); fprintf(ofp, "closepath\n"); fprintf(ofp, "fill\n"); fprintf(ofp, "} def\n"); /* PS definition of a flush right print */ fprintf(ofp, "\n%% flush right show\n"); fprintf(ofp, "/centershow {\n"); fprintf(ofp, " dup stringwidth pop %% get length of string\n"); fprintf(ofp, " neg 0 rmoveto %% move width to left\n"); fprintf(ofp, " show\n"); fprintf(ofp, "} def\n"); fprintf(ofp, "\n%% centered show\n"); /* PS definition of a centered print */ fprintf(ofp, "/centershow {\n"); fprintf(ofp, " dup stringwidth pop %% get length of string\n"); fprintf(ofp, " -2 div %% devide length by -2\n"); fprintf(ofp, " 0 rmoveto %% move half width to left\n"); fprintf(ofp, " show\n"); fprintf(ofp, "} def\n"); fprintf(ofp, "%% preamble\n"); fprintf(ofp, "/Helvetica findfont\n"); fprintf(ofp, "12 scalefont\n"); fprintf(ofp, "setfont\n"); fprintf(ofp, "%% 0/0 for triangle of triangles\n"); fprintf(ofp, "0.9 inch 3 inch translate\n"); fprintf(ofp, "%% first triangle (the one with dots)\n"); fprintf(ofp, "0.6 tl 1.2 tl 0.8660254038 mul translate\n"); fprintf(ofp, "newpath\n"); fprintf(ofp, " 0.0 tl 0.0 tl moveto\n"); fprintf(ofp, " 1.0 tl 0.0 tl lineto\n"); fprintf(ofp, " 0.5 tl 0.8660254038 tl lineto\n"); fprintf(ofp, "closepath\n"); fprintf(ofp, "stroke\n"); if (numclust == 4) { /* four cluster analysis */ fprintf(ofp, "%% label corners\n"); fprintf(ofp, "0.5 tl 0.9 tl moveto\n"); /* old: 0.375 0.9 */ fprintf(ofp, "((a,b)-(c,d)) centershow %% CHANGE HERE IF NECESSARY\n"); fprintf(ofp, "-0.045 tl -0.08 tl moveto\n"); /* old: -0.16 -0.08 */ fprintf(ofp, "((a,d)-(b,c)) centershow %% CHANGE HERE IF NECESSARY\n"); fprintf(ofp, "1.045 tl -0.08 tl moveto\n"); /* old: -0.92 -0.08 */ fprintf(ofp, "((a,c)-(b,d)) centershow %% CHANGE HERE IF NECESSARY\n"); } if (numclust == 3) { /* three cluster analysis */ fprintf(ofp, "%% label corners\n"); fprintf(ofp, "0.5 tl 0.9 tl moveto\n"); /* old: 0.375 0.9 */ fprintf(ofp, "((a,b)-(c,c)) centershow %% CHANGE HERE IF NECESSARY\n"); fprintf(ofp, "-0.045 tl -0.08 tl moveto\n"); /* old: -0.16 -0.08 */ fprintf(ofp, "((a,c)-(b,c)) centershow %% CHANGE HERE IF NECESSARY\n"); fprintf(ofp, "1.045 tl -0.08 tl moveto\n"); /* old: -0.92 -0.08 */ fprintf(ofp, "((a,c)-(b,c)) centershow %% CHANGE HERE IF NECESSARY\n"); } if (numclust == 2) { /* two cluster analysis */ fprintf(ofp, "%% label corners\n"); fprintf(ofp, "0.5 tl 0.9 tl moveto\n"); /* old: 0.375 0.9 */ fprintf(ofp, "((a,a)-(b,b)) centershow %% CHANGE HERE IF NECESSARY\n"); fprintf(ofp, "-0.045 tl -0.08 tl moveto\n"); /* old: -0.16 -0.08 */ fprintf(ofp, "((a,b)-(a,b)) centershow %% CHANGE HERE IF NECESSARY\n"); fprintf(ofp, "1.045 tl -0.08 tl moveto\n"); /* old: -0.92 -0.08 */ fprintf(ofp, "((a,b)-(a,b)) centershow %% CHANGE HERE IF NECESSARY\n"); } } /* initps */ /* plot one point of likelihood mapping analysis */ void plotlmpoint(FILE *ofp, double w1, double w2) { fprintf(ofp,"%.10f tl %.10f tl dot\n", 0.5*w1 + w2, w1*0.8660254038); } /* plotlmpoint */ /* last lines of EPSF likelihood mapping file */ void finishps(FILE *ofp) { fprintf(ofp, "stroke\n"); fprintf(ofp, "%% second triangle (the one with 3 basins)\n"); fprintf(ofp, "/secondtriangle {\n"); fprintf(ofp, "newpath\n"); fprintf(ofp, " 0.0 tl 0.0 tl moveto\n"); fprintf(ofp, " 1.0 tl 0.0 tl lineto\n"); fprintf(ofp, " 0.5 tl 0.8660254038 tl lineto\n"); fprintf(ofp, "closepath\n"); fprintf(ofp, "stroke\n"); fprintf(ofp, "newpath\n"); fprintf(ofp, " 0.50 tl 0.2886751346 tl moveto\n"); fprintf(ofp, " 0.50 tl 0.0000000000 tl lineto\n"); fprintf(ofp, "stroke\n"); fprintf(ofp, "newpath\n"); fprintf(ofp, " 0.50 tl 0.2886751346 tl moveto\n"); fprintf(ofp, " 0.25 tl 0.4330127019 tl lineto\n"); fprintf(ofp, "stroke\n"); fprintf(ofp, "newpath\n"); fprintf(ofp, " 0.50 tl 0.2886751346 tl moveto\n"); fprintf(ofp, " 0.75 tl 0.4330127019 tl lineto\n"); fprintf(ofp, "stroke\n"); fprintf(ofp, "0.44 tl 0.5 tl moveto %% up\n"); fprintf(ofp, "(%.1f%%) show\n", (double) ar1*100.0/Numquartets); fprintf(ofp, "0.25 tl 0.15 tl moveto %% down left\n"); fprintf(ofp, "(%.1f%%) show\n", (double) ar3*100.0/Numquartets); fprintf(ofp, "0.63 tl 0.15 tl moveto %% down right\n"); fprintf(ofp, "(%.1f%%) show\n", (double) ar2*100.0/Numquartets); fprintf(ofp, "} def\n"); fprintf(ofp, "%% third triangle (the one with 7 basins)\n"); fprintf(ofp, "/thirdtriangle {\n"); fprintf(ofp, "newpath\n"); fprintf(ofp, " 0.0 tl 0.0 tl moveto\n"); fprintf(ofp, " 1.0 tl 0.0 tl lineto\n"); fprintf(ofp, " 0.5 tl 0.8660254038 tl lineto\n"); fprintf(ofp, "closepath\n"); fprintf(ofp, "stroke\n"); fprintf(ofp, "newpath\n"); fprintf(ofp, " 0.25 tl 0.1443375673 tl moveto\n"); fprintf(ofp, " 0.75 tl 0.1443375673 tl lineto\n"); fprintf(ofp, " 0.50 tl 0.5773502692 tl lineto\n"); fprintf(ofp, "closepath\n"); fprintf(ofp, "stroke\n"); fprintf(ofp, "newpath\n"); fprintf(ofp, " 0.125 tl 0.2165063509 tl moveto\n"); fprintf(ofp, " 0.250 tl 0.1443375673 tl lineto\n"); fprintf(ofp, "stroke\n"); fprintf(ofp, "newpath\n"); fprintf(ofp, " 0.375 tl 0.6495190528 tl moveto\n"); fprintf(ofp, " 0.500 tl 0.5773502692 tl lineto\n"); fprintf(ofp, "stroke\n"); fprintf(ofp, "newpath\n"); fprintf(ofp, " 0.625 tl 0.6495190528 tl moveto\n"); fprintf(ofp, " 0.500 tl 0.5773502692 tl lineto\n"); fprintf(ofp, "stroke\n"); fprintf(ofp, "newpath\n"); fprintf(ofp, " 0.875 tl 0.2165063509 tl moveto\n"); fprintf(ofp, " 0.750 tl 0.1443375673 tl lineto\n"); fprintf(ofp, "stroke\n"); fprintf(ofp, "newpath\n"); fprintf(ofp, " 0.750 tl 0.00 tl moveto\n"); fprintf(ofp, " 0.750 tl 0.1443375673 tl lineto\n"); fprintf(ofp, "stroke\n"); fprintf(ofp, "newpath\n"); fprintf(ofp, " 0.250 tl 0.00 tl moveto\n"); fprintf(ofp, " 0.250 tl 0.1443375673 tl lineto\n"); fprintf(ofp, "stroke\n"); fprintf(ofp, "0.42 tl 0.66 tl moveto %% up\n"); fprintf(ofp, "(%.1f%%) show\n", (double) reg1*100.0/Numquartets); fprintf(ofp, "0.07 tl 0.05 tl moveto %% down left\n"); fprintf(ofp, "(%.1f%%) show\n", (double) reg3*100.0/Numquartets); fprintf(ofp, "0.77 tl 0.05 tl moveto %% down right\n"); fprintf(ofp, "(%.1f%%) show\n", (double) reg2*100.0/Numquartets); fprintf(ofp, "0.43 tl 0.05 tl moveto %% down side\n"); fprintf(ofp, "(%.1f%%) show\n", (double) reg5*100.0/Numquartets); fprintf(ofp, "0.43 tl 0.28 tl moveto %% center\n"); fprintf(ofp, "(%.1f%%) show\n", (double) reg7*100.0/Numquartets); fprintf(ofp, "gsave\n"); fprintf(ofp, "-60 rotate\n"); fprintf(ofp, "-0.07 tl 0.77 tl moveto %% right side\n"); fprintf(ofp, "(%.1f%%) show\n", (double) reg4*100.0/Numquartets); fprintf(ofp, "grestore\n"); fprintf(ofp, "gsave\n"); fprintf(ofp, "60 rotate\n"); fprintf(ofp, "0.4 tl -0.09 tl moveto %% left side\n"); fprintf(ofp, "(%.1f%%) show\n", (double) reg6*100.0/Numquartets); fprintf(ofp, "grestore\n"); fprintf(ofp, "} def\n"); fprintf(ofp, "%% print the other two triangles\n"); fprintf(ofp, "-0.6 tl -1.2 tl 0.8660254038 mul translate\n"); fprintf(ofp, "secondtriangle\n"); fprintf(ofp, "1.2 tl 0 translate\n"); fprintf(ofp, "thirdtriangle\n"); fprintf(ofp, "showpage\n"); fprintf(ofp, "%%%%EOF\n"); } /* finishps */ /* computes LM point from the three log-likelihood values, plots the point, and does some statistics */ void makelmpoint(FILE *fp, double b1, double b2, double b3) { double w1, w2, w3, temp; unsigned char qpbranching; double temp1, temp2, temp3, onethird; double templog; unsigned char discreteweight[3], treebits[3]; onethird = 1.0/3.0; treebits[0] = (unsigned char) 1; treebits[1] = (unsigned char) 2; treebits[2] = (unsigned char) 4; /* sort in descending order */ qweight[0] = b1; qweight[1] = b2; qweight[2] = b3; sort3doubles(qweight, qworder); /* compute Bayesian weights */ templog = qweight[qworder[1]]-qweight[qworder[0]]; if(templog < -TP_MAX_EXP_DIFF) /* possible, since 1.0+exp(>36) == 1.0 */ qweight[qworder[1]] = 0.0; else qweight[qworder[1]] = exp(templog); templog = qweight[qworder[2]]-qweight[qworder[0]]; if(templog < -TP_MAX_EXP_DIFF) /* possible, since 1.0+exp(>36) == 1.0 */ qweight[qworder[2]] = 0.0; else qweight[qworder[2]] = exp(templog); qweight[qworder[0]] = 1.0; temp = qweight[0] + qweight[1] + qweight[2]; qweight[0] = qweight[0]/temp; qweight[1] = qweight[1]/temp; qweight[2] = qweight[2]/temp; /* plot one point in likelihood mapping triangle */ w1 = qweight[0]; w2 = qweight[1]; w3 = qweight[2]; plotlmpoint(fp, w1, w2); /* check areas 1,2,3 */ if (treebits[qworder[0]] == 1) ar1++; else if (treebits[qworder[0]] == 2) ar2++; else ar3++; /* check out regions 1,2,3,4,5,6,7 */ /* 100 distribution */ temp1 = 1.0 - qweight[qworder[0]]; sqdiff[0] = temp1*temp1 + qweight[qworder[1]]*qweight[qworder[1]] + qweight[qworder[2]]*qweight[qworder[2]]; discreteweight[0] = treebits[qworder[0]]; /* 110 distribution */ temp1 = 0.5 - qweight[qworder[0]]; temp2 = 0.5 - qweight[qworder[1]]; sqdiff[1] = temp1*temp1 + temp2*temp2 + qweight[qworder[2]]*qweight[qworder[2]]; discreteweight[1] = treebits[qworder[0]] + treebits[qworder[1]]; /* 111 distribution */ temp1 = onethird - qweight[qworder[0]]; temp2 = onethird - qweight[qworder[1]]; temp3 = onethird - qweight[qworder[2]]; sqdiff[2] = temp1 * temp1 + temp2 * temp2 + temp3 * temp3; discreteweight[2] = (unsigned char) 7; /* sort in descending order */ sort3doubles(sqdiff, sqorder); qpbranching = (unsigned char) discreteweight[sqorder[2]]; if (qpbranching == 1) { reg1++; if (w2 < w3) reg1l++; else reg1r++; } if (qpbranching == 2) { reg2++; if (w1 < w3) reg2d++; else reg2u++; } if (qpbranching == 4) { reg3++; if (w1 < w2) reg3d++; else reg3u++; } if (qpbranching == 3) { reg4++; if (w1 < w2) reg4d++; else reg4u++; } if (qpbranching == 6) { reg5++; if (w2 < w3) reg5l++; else reg5r++; } if (qpbranching == 5) { reg6++; if (w1 < w3) reg6d++; else reg6u++; } if (qpbranching == 7) reg7++; } /* makelmpoint */ #if 0 /* TODO: move to treetest.c */ #define MINKHDIFF 0.01 /* TODO: move to treetest.c */ /*****************************************************************************/ /* ELW/SR Test (Expected Likelihood Weights, Strimmer & Rambaut, 2002) */ /*****************************************************************************/ void elw_test(ivector Alias, dmatrix allsites, int numutrees, int numsites, double siglevel, int numboots, ivector *elw_test_passed, dvector *elw_Support) { /* * Determine posterior probabilties and support values * for each hypothesis and store results in public arrays * posterior, support etc which will automatically be * created by this procedure. * * allsites log-likelihoods of each pattern * Alias map of patterns to sites in sequence * numboots number of bootstraps */ dvector deltaL; /* delta of likelihoods (double[numH]) */ dvector elw_support; /* (double[numH]) */ dvector posterior; /* (double[numH]) */ ivector likelihoodOrder; /* (int[numH]) */ ivector supportOrder; /* (int[numH]) */ dvector rs; /* (int[numH]) */ double sum1; double sum; int numH; /* number of hypotheses */ int numSites; /* number of sites */ int s, p; int i, j, k; /* int j; */ double maxL; double maxLogL; ivector sr_test_res; /* [numutrees]; */ int elw_numboots = 1000; /* number of hypothesis */ numH = numutrees; /* allocate public arrays */ deltaL = new_dvector(numH); elw_support = new_dvector(numH); posterior = new_dvector(numH); likelihoodOrder = new_ivector(numH); supportOrder = new_ivector(numH); sr_test_res = new_ivector(numutrees); *elw_test_passed = sr_test_res; *elw_Support = elw_support; /* number of sites */ numSites = numsites; /******************************************/ /* Compute log-likelihoods, their order, */ /* their deltas and their posteriors */ /******************************************/ /* initialize delta vector for each tree */ for (j = 0; j < numSites; j++) { if (Alias == NULL) { p = j; } else { p = Alias[j]; } for (k = 0; k < numH; k++) { deltaL[k] -= allsites[k][p]; } } /* sort likelihoods -> sorted index list likelihoodOrder */ /* insertion sort */ { int tmp; int idx; for (k=0; k < numH; k++) likelihoodOrder[k] = k; for (j=0; j < numH-1; j++) { idx=j; for (k=j+1; k < numH; k++) { if (deltaL[likelihoodOrder[k]] < deltaL[likelihoodOrder[idx]]) idx=k; } tmp = likelihoodOrder[j]; likelihoodOrder[j] = likelihoodOrder[idx]; likelihoodOrder[idx] = tmp; } } /* Compute deltas */ maxL= -deltaL[likelihoodOrder[0]]; for (j = 0; j < numH; j++) { deltaL[j] = -(deltaL[j]+maxL); } /* compute posterior probabilities */ sum1 = 0.0; for (j = 0; j < numH; j++) { posterior[j] = exp(deltaL[j]); sum1 += posterior[j]; } for (j = 0; j < numH; j++) { posterior[j] = posterior[j]/sum1; } /* reverse sign of delta L */ for (j = 0; j < numH; j++) { deltaL[j] = -deltaL[j]; } deltaL[likelihoodOrder[0]] = 0.0; /* Bootstrap/Resample data */ /***************************/ /* temporary memory */ rs = new_dvector(numH); /* MersenneTwisterFast mt = new MersenneTwisterFast(); */ for (i = 0; i < elw_numboots; i++) { /* num bootstraps */ for (k = 0; k < numH; k++) { rs[k] = 0; } for (j = 0; j < numSites; j++) { /* bootstrapping sites for ...*/ /* int s = mt.nextInt(numSites); */ s = randominteger(numSites); if (Alias == NULL) { p = s; } else { p = Alias[s]; } for (k = 0; k < numH; k++) { /* ...each utree */ /* rs[k] += pLogL[k][p]; */ rs[k] += allsites[k][p]; } } /* find ml hypothesis */ /* maxLogL = findMax(rs); */ { int best = 0; /* can be removed (HAS) */ int idx; double max = rs[0]; for (idx = 1; idx < numH; idx++) { if (rs[idx] > max) { best = idx; /* can be removed (HAS) */ max = rs[idx]; } } maxLogL = max; } /* compute log-likelihood difference */ for (k = 0; k < numH; k++) { rs[k] = rs[k] - maxLogL; } /* compute posteriors and sum over resampled data set */ sum = 0.0; for (k = 0; k < numH; k++) { rs[k] = exp(rs[k]); sum += rs[k]; } for (k = 0; k < numH; k++) { elw_support[k] += rs[k]/sum; } } /* compute support values */ for (j = 0; j < numH; j++) { elw_support[j] = elw_support[j]/elw_numboots; } /* determine order of elw_support (smallest->largest) */ /* HeapSort.sort(elw_support, supportOrder); */ { int tmp; int idx; for (k=0; k < numH; k++) supportOrder[k] = k; for (j=0; j < numH-1; j++) { idx=j; for (k=j+1; k < numH; k++) { if (elw_support[supportOrder[k]] > elw_support[supportOrder[idx]]) idx=k; } tmp = supportOrder[j]; supportOrder[j] = supportOrder[idx]; supportOrder[idx] = tmp; } } sum = 0.0; for (k=0; k maxLogL) { bestH = i; maxLogL = sh_logL[i]; } } /* compute log-likelihood differences to best hypothesis */ for (i = 0; i < numH; i++) { sh_delta[i] = sh_logL[bestH]-sh_logL[i]; } /* allocate temporary memory for resampling procedure */ bs = new_dmatrix(numH,sh_numboots); /* Resample data */ /* MersenneTwisterFast mt = new MersenneTwisterFast(); */ for (i = 0; i < sh_numboots; i++) { for (j = 0; j < numSites; j++) { /* int s = mt.nextInt(numSites); */ s = randominteger(numSites); if (Alias == NULL) { p = s; } else { p = Alias[s]; } for (k = 0; k < numH; k++) { /* rs[k][i] += pLogL[k][p]; */ bs[k][i] += allsites[k][p]; } } } /* center resampled log-likelihoods */ for (i = 0; i < numH; i++) { /* double m = DiscreteStatistics.mean(rs[i]); */ m = 0.0; for (j = 0; j < sh_numboots; j++) { m += bs[i][j]; } m /= sh_numboots; for (j = 0; j < sh_numboots; j++) { bs[i][j] = bs[i][j] - m; } } /* compute resampled log-likelihood differences */ for (i = 0; i < sh_numboots; i++) { /* double max = findMaxInColumn(rs, i); */ { best = 0; colmax = bs[0][i]; for (j = 1; j < numH; j++) { if (bs[j][i] > colmax) { best = j; colmax = bs[j][i]; } } } for (j = 0; j < numH; j++) { bs[j][i] = colmax - bs[j][i]; } } /* compute p-values for each hypothesis */ for (i = 0; i < numH; i++) { count = 0; for (j = 0; j < sh_numboots; j++) { if (bs[i][j] >= sh_delta[i]) { count++; } } sh_pval[i] = (double) count/(double) sh_numboots; if (sh_pval[i] >= sh_prob) { sh_test_res[i] = 1; } else { sh_test_res[i] = 0; } } /* free memory */ free_dmatrix(bs); free_dvector(sh_logL); } /* sh_test */ /* TODO: move to treetest.c */ /* print tree statistics */ void printtreestats(FILE *ofp) { int i, j; /* counter variables */ int besttree; /* best tree */ /* for the KH Test (Kishino & Hasegawa, 1989) */ double bestlkl; /* best likelihood */ double difflkl; /* best likelihood difference */ double difflklps; /* best likelihood difference per site */ double temp; double sum; /* variables for the SH Test (Shimodaira & Hasegawa, 1999) */ dvector sh_pval; /* corresponding p-value */ double sh_prob = .05; /* significance level */ int sh_numboots = 1000; /* number of bootstrap samples */ ivector sh_test_res; /* result vector [numutrees]; */ /* variables for the ELW/SR Test (Expected Likelihood Weights) */ /* (Strimmer & Rambaut, 2002) */ dvector elw_support; /* = new double[numH; */ ivector elw_test_res; /* result vector [numutrees]; */ int elw_numboots = 1000; /* number of bootstrap samples */ double elw_prob = .05; /* significance level */ /* variables for the one-sided KH Test using SH */ dvector kh1_pval_tmp; /* temp p-value arry for pairwise SH */ ivector kh1_test_res_tmp; /* temp result arry for pairwise SH */ dvector kh1_pval; /* p-values */ ivector kh1_test_res; /* result vector [numutrees]; */ dvector kh1_allsites_tmp[2]; /* temp arry for pairwise SH test */ int kh1_numboots = 1000; /* number of bootstrap samples */ double kh1_prob = .05; /* significance level */ /* find best tree */ besttree = 0; bestlkl = ulkl[0]; for (i = 1; i < numutrees; i++) { if (ulkl[i] > bestlkl) { besttree = i; bestlkl = ulkl[i]; } } /* one sided KH = pairwise SH test between tree and besttree */ fprintf(STDOUT, "Performing single sided KH test.\n"); fflush(STDOUT); kh1_pval = new_dvector(numutrees); kh1_test_res = new_ivector(numutrees); kh1_allsites_tmp[0] = allsites[besttree]; /* set best tree */ for (i = 0; i < numutrees; i++) { if (i == besttree) { /* if best tree -> no test */ kh1_pval[i] = 1.0; kh1_test_res[i] = 1; } else { /* other wise test pairwise SH */ kh1_allsites_tmp[1] = allsites[i]; /* set site log-lh */ sh_test(Alias, kh1_allsites_tmp, 2, Maxsite, kh1_prob, kh1_numboots, &kh1_test_res_tmp, &kh1_pval_tmp); /* pairwise SH */ kh1_pval[i] = kh1_pval_tmp[1]; /* store p-value */ kh1_test_res[i] = kh1_test_res_tmp[1]; /* save result */ } } free_ivector(kh1_test_res_tmp); /* moved out of loop */ free_dvector(kh1_pval_tmp); /* ELW */ fprintf(STDOUT, "Performing ELW test.\n"); fflush(STDOUT); elw_test(Alias, allsites, numutrees, Maxsite, elw_prob, elw_numboots, &elw_test_res, &elw_support); /* SH */ fprintf(STDOUT, "Performing SH test.\n"); fflush(STDOUT); sh_test(Alias, allsites, numutrees, Maxsite, sh_prob, sh_numboots, &sh_test_res, &sh_pval); /*****************************************************************************/ /* two-sided KH Test (Kishino & Hasegawa, 1989) */ /* and output */ /*****************************************************************************/ fprintf(ofp, "\n\nCOMPARISON OF USER TREES (NO CLOCK)\n\n"); # ifdef KHTWOSIDED fprintf(ofp, "Tree log L difference S.E. Sig. worse p-1sKH p-SH c-ELW \n"); fprintf(ofp, "-------------------------------------------------------------------------------\n"); # else fprintf(ofp, "Tree log L difference S.E. p-1sKH p-SH c-ELW 2sKH\n"); fprintf(ofp, "-------------------------------------------------------------------------------\n"); # endif for (i = 0; i < numutrees; i++) { difflkl = ulkl[besttree]-ulkl[i]; fprintf(ofp, "%2d %10.4f %8.4f ", i+1, ulkl[i], difflkl); /* fprintf(ofp, "%2d %10.2f %8.2f ", i+1, ulkl[i], difflkl); */ if (i == besttree) { # ifdef KHTWOSIDED fprintf(ofp, " <-------------- best "); # else fprintf(ofp, " <---- best "); /* fprintf(ofp, " <---- best "); */ # endif if (kh1_test_res[i] == 1) fprintf(ofp, " %6.4f +", kh1_pval[i]); else fprintf(ofp, " %6.4f -", kh1_pval[i]); if (sh_test_res[i] == 1) fprintf(ofp, " %6.4f +", sh_pval[i]); else fprintf(ofp, " %6.4f -", sh_pval[i]); if (elw_test_res[i] == 1) fprintf(ofp, " %6.4f +", elw_support[i]); else fprintf(ofp, " %6.4f -", elw_support[i]); # ifdef KHTWOSIDED # else fprintf(ofp, " best"); # endif } else { /* compute variance of Log L differences over sites */ #ifndef USE_WINDOWS difflklps = difflkl/(double)Maxsite; #else difflklps = difflkl/(double)alimaxsite; #endif /* compute std. error of sample mean with curvature method */ sum = 0.0; for (j = 0; j < Numptrn; j++) { temp = allsites[besttree][j] - allsites[i][j] - difflklps; sum += temp*temp*Weight[j]; } #ifndef USE_WINDOWS sum = sqrt( fabs(sum/(Maxsite-1.0)*Maxsite) ); #else sum = sqrt(fabs(sum/(alimaxsite-1.0)*alimaxsite)); #endif # ifdef KHTWOSIDED fprintf(ofp, "%11.2f ", sum); if (difflkl > 1.96*sum) fprintf(ofp, "yes "); else fprintf(ofp, "no "); # else fprintf(ofp, "%11.4f ", sum); /* fprintf(ofp, "%11.2f ", sum); */ # endif if (kh1_test_res[i] == 1) fprintf(ofp, " %6.4f +", kh1_pval[i]); else fprintf(ofp, " %6.4f -", kh1_pval[i]); if (sh_test_res[i] == 1) fprintf(ofp, " %6.4f +", sh_pval[i]); else fprintf(ofp, " %6.4f -", sh_pval[i]); if (elw_test_res[i] == 1) fprintf(ofp, " %6.4f +", elw_support[i]); else fprintf(ofp, " %6.4f -", elw_support[i]); # ifdef KHTWOSIDED # else if (difflkl > 1.96*sum) fprintf(ofp, " - (diff=%.4f 1.96*sum=%.4e)", difflkl, 1.96*sum); else fprintf(ofp, " + (diff=%.4f 1.96*sum=%.4e)", difflkl, 1.96*sum); #if 0 if (difflkl > 1.96*sum) fprintf(ofp, " -"); else fprintf(ofp, " +"); #endif # endif } fprintf(ofp, "\n"); } fprintf(ofp, "\nThe columns show the results and p-values of the following tests:\n"); fprintf(ofp, "1sKH - one sided KH test based on pairwise SH tests (Shimodaira-Hasegawa\n"); fprintf(ofp, " 2000, Goldman et al., 2001, Kishino-Hasegawa 1989)\n"); fprintf(ofp, "SH - Shimodaira-Hasegawa test (2000)\n"); fprintf(ofp, "ELW - Expected Likelihood Weight (Strimmer-Rambaut 2002)\n"); fprintf(ofp, "2sKH - two sided Kishino-Hasegawa test (1989)\n"); fprintf(ofp, "\n"); fprintf(ofp, "Plus signs denote the confidence sets. Minus signs denote significant\n"); fprintf(ofp, "exclusion. All tests used 5%% significance level. 1sKH, SH, and ELW\n"); fprintf(ofp, "performed 1000 resamplings using the RELL method.\n"); if (compclock) { /* find best tree */ besttree = 0; bestlkl = ulklc[0]; for (i = 1; i < numutrees; i++) if (ulklc[i] > bestlkl) { besttree = i; bestlkl = ulklc[i]; } /* one sided KH */ fprintf(STDOUT, "Performing single sided KH test (clock).\n"); fflush(STDOUT); kh1_pval = new_dvector(numutrees); kh1_test_res = new_ivector(numutrees); kh1_allsites_tmp[0] = allsitesc[besttree]; for (i = 0; i < numutrees; i++) { if (i != besttree) { kh1_allsites_tmp[1] = allsitesc[i]; sh_test(Alias, kh1_allsites_tmp, 2, Maxsite, kh1_prob, kh1_numboots, &kh1_test_res_tmp, &kh1_pval_tmp); kh1_pval[i] = kh1_pval_tmp[1]; kh1_test_res[i] = kh1_test_res_tmp[1]; free_ivector(kh1_test_res_tmp); free_dvector(kh1_pval_tmp); } else { kh1_pval[i] = 1.0; kh1_test_res[i] = 1; } } /* ELW */ fprintf(STDOUT, "Performing ELW test (clock).\n"); fflush(STDOUT); elw_test(Alias, allsitesc, numutrees, Maxsite, elw_prob, elw_numboots, &elw_test_res, &elw_support); /* SH */ fprintf(STDOUT, "Performing SH test (clock).\n"); fflush(STDOUT); sh_test(Alias, allsitesc, numutrees, Maxsite, sh_prob, sh_numboots, &sh_test_res, &sh_pval); fprintf(ofp, "\n\nCOMPARISON OF USER TREES (WITH CLOCK)\n\n"); # ifdef KHTWOSIDED fprintf(ofp, "Tree log L difference S.E. Sig. worse p-1sKH p-SH c-ELW \n"); fprintf(ofp, "-------------------------------------------------------------------------------\n"); # else fprintf(ofp, "Tree log L difference S.E. p-1sKH p-SH c-ELW 2sKH\n"); fprintf(ofp, "-------------------------------------------------------------------------------\n"); # endif for (i = 0; i < numutrees; i++) { difflkl = ulklc[besttree]-ulklc[i]; fprintf(ofp, "%2d %10.2f %8.2f ", i+1, ulklc[i], difflkl); if (i == besttree) { # ifdef KHTWOSIDED fprintf(ofp, " <-------------- best "); # else fprintf(ofp, " <---- best "); # endif if (kh1_test_res[i] == 1) fprintf(ofp, " %6.4f +", kh1_pval[i]); else fprintf(ofp, " %6.4f -", kh1_pval[i]); if (sh_test_res[i] == 1) fprintf(ofp, " %6.4f +", sh_pval[i]); else fprintf(ofp, " %6.4f -", sh_pval[i]); if (elw_test_res[i] == 1) fprintf(ofp, " %6.4f +", elw_support[i]); else fprintf(ofp, " %6.4f -", elw_support[i]); # ifdef KHTWOSIDED # else fprintf(ofp, " best"); # endif } else { /* compute variance of Log L differences over sites */ #ifndef USE_WINDOWS difflklps = difflkl/(double)Maxsite; #else difflklps = difflkl/(double)alimaxsite; #endif sum = 0.0; for (j = 0; j < Numptrn; j++) { temp = allsitesc[besttree][j] - allsitesc[i][j] - difflklps; sum += temp*temp*Weight[j]; } #ifndef USE_WINDOWS sum = sqrt(fabs(sum/(Maxsite-1.0)*Maxsite)); #else sum = sqrt(fabs(sum/(alimaxsite-1.0)*alimaxsite)); #endif # ifdef KHTWOSIDED fprintf(ofp, "%11.2f ", sum); if (difflkl > 1.96*sum) fprintf(ofp, "yes "); else fprintf(ofp, "no "); # else fprintf(ofp, "%11.2f ", sum); # endif if (kh1_test_res[i] == 1) fprintf(ofp, " %6.4f +", kh1_pval[i]); else fprintf(ofp, " %6.4f -", kh1_pval[i]); if (sh_test_res[i] == 1) fprintf(ofp, " %6.4f +", sh_pval[i]); else fprintf(ofp, " %6.4f -", sh_pval[i]); if (elw_test_res[i] == 1) fprintf(ofp, " %6.4f +", elw_support[i]); else fprintf(ofp, " %6.4f -", elw_support[i]); # ifdef KHTWOSIDED # else if (difflkl > 1.96*sum) fprintf(ofp, " -"); else fprintf(ofp, " +"); # endif } fprintf(ofp, "\n"); } fprintf(ofp, "\nThe columns show the results and p-values of the following tests:\n"); fprintf(ofp, "1sKH - one sided KH test based on pairwise SH tests (Shimodaira-Hasegawa\n"); fprintf(ofp, " 2000, Goldman et al., 2001, Kishino-Hasegawa 1989)\n"); fprintf(ofp, "SH - Shimodaira-Hasegawa test (2000)\n"); fprintf(ofp, "ELW - Expected Likelihood Weight (Strimmer-Rambaut 2002)\n"); fprintf(ofp, "2sKH - two sided Kishino-Hasegawa test (1989)\n"); fprintf(ofp, "\n"); fprintf(ofp, "Plus signs denote the confidence sets. Minus signs denote significant\n"); fprintf(ofp, "exclusion. All tests used 5%% significance level. 1sKH, SH, and ELW\n"); fprintf(ofp, "performed 1000 resamplings using the RELL method.\n"); #if 0 fprintf(ofp, "\nColmn 5 gives the results of the (old) two-sided Kishino-Hasegawa test \n"); fprintf(ofp, "following Kishino and Hasegawa (1989). It tests whether a likelihood is \n"); fprintf(ofp, "significantly worse than the best one, marked with 'best'. This test should \n"); fprintf(ofp, "only be used for data not having been determined with the data tested on.\n"); fprintf(ofp, "1sKH is the one-sided KH test (Goldman et al., 2001). It is applicable\n"); fprintf(ofp, "to test whether likelihoods are worse than the lielihood of the ML tree.\n"); fprintf(ofp, "SH tests for the best trees (Shimodaira and Hasegawa, 2000).\n"); fprintf(ofp, "Note that KH, 1sKH, and SH assume to have the 'true' topologies among the tested.\n"); fprintf(ofp, "ELW (Expected likelihood weights) seems to work even without this restriction\n"); fprintf(ofp, "(Strimmer and Rambaut, 2002). Still plausible trees should be among the tested.\n"); fprintf(ofp, "For 1sKH, SH, and ELW plus signs '+' mark the topologies belonging to the\n"); fprintf(ofp, "confidence sets the numbers give the p-values (1sKH and SH) or the confidence\n"); fprintf(ofp, "weight (ELW).\n"); fprintf(ofp, "All tests used 5%% significance level. 1sKH, SH, and ELW used 1000 resamplings.\n"); #endif } } /* printtreestats */ #endif /********************************************************/ /* time stamp */ void timestamp(FILE* ofp) { double timespan; double cpuspan; timespan = difftime(Stoptime, Starttime); cpuspan = ((double) (Stopcpu - Startcpu) / CLOCKS_PER_SEC); fprintf(ofp, "\n\nTIME STAMP\n\n"); fprintf(ofp, "Date and time: %s", asctime(localtime(&Starttime)) ); fprintf(ofp, "Runtime (excl. input) : %.0f seconds (= %.1f minutes = %.1f hours)\n", timespan, timespan/60., timespan/3600.); fprintf(ofp, "Runtime (incl. input) : %.0f seconds (= %.1f minutes = %.1f hours)\n", fulltime, fulltime/60., fulltime/3600.); #ifdef TIMEDEBUG fprintf(ofp, "CPU time (incl. input): %.0f seconds (= %.1f minutes = %.1f hours)\n\n", fullcpu, fullcpu/60., fullcpu/3600.); #endif /* TIMEDEBUG */ } /* timestamp */ /* SONJA #include "sonja.c" */ /***************************************************************************/ /*** ***/ /*** Sonja's distance problem ;-) ***/ /*** ***/ /***************************************************************************/ #ifdef SONJA /* routines to compute the distances in the tree */ /* # include "sonja.c" */ /* collect distances from the subtree rooted by np */ void subtree2dist(Node *np, /* subtree root */ ivector nodefound, /* leaves in this subtree */ dvector nodedist, /* distances leaf <-> np */ dmatrix distmat, /* dist matrix between leaves */ imatrix distdone) /* done flags */ { int n, m; ivector foundbelow; Node *tp; /* external node = leaf */ if (np->isop == NULL) { # ifdef DEBUGTREEDIST fprintf(stderr, "e%d: len=%.6f\n", np->number, np->length); # endif /* nodedist[np->number] = np->length; */ nodefound[np->number] = 1; return; } else { /* if not external node */ # ifdef DEBUGTREEDIST fprintf(stderr, "i%d: len=%.6f\n", np->number, np->length); # endif foundbelow = new_ivector(Maxspc); /* for every branch at the inner node */ tp = np->isop; while (tp != np) { for (n = 0; n < Maxspc; n++) foundbelow[n] = 0; subtree2dist(tp->kinp, foundbelow, nodedist, distmat, distdone); for (n = 0; n < Maxspc; n++) { if (foundbelow[n] == 1) { # ifdef DEBUGTREEDIST fprintf(stderr, " +++i%d: nd%d=%.5f+%.5f=%.5f\n", np->number, n, nodedist[n], tp->length, nodedist[n]+tp->length); # endif nodefound[n] = 1; nodedist[n] += tp->length; } } tp = tp->isop; } /* while tp != np */ for (n = 0; n < Maxspc; n++) { for (m = n+1; m < Maxspc; m++) { if ((distdone[n][m]!=1) && (nodefound[n]==1) && (nodefound[m]==1)) { distmat[n][m] = nodedist[n] + nodedist[m]; distmat[m][n] = distmat[n][m]; distdone[n][m] = 1; distdone[m][n] = 1; } /* if */ } /* for m */ } /* for n */ free (foundbelow); } /* if not external node */ } /***************************************************************************/ /* collect all distances from the current tree */ void tree2dist(dmatrix distmat) { ivector nodefound; imatrix distdone; dvector nodedist; int n, m; nodefound = new_ivector(Maxspc); distdone = new_imatrix(Maxspc,Maxspc); nodedist = new_dvector(Maxspc); for (n = 0; n < Maxspc; n++) { nodedist[n] = 0.0; nodefound[n] = 0; for (m = n+1; m < Maxspc; m++) { if (n==m) { distmat[n][m] = 0.0; distdone[n][m] = 1; } else { distmat[n][m] = 0.0; distmat[m][n] = 0.0; distdone[n][m] = 0; distdone[m][n] = 0; } } /* for m */ } /* for n */ /* we are NOT on a leaf, because root -> collect */ subtree2dist(Ctree->ebrnchp[outgroup]->kinp, nodefound, nodedist, distmat, distdone); /* compute distances to the root */ m = outgroup; for (n = 0; n < Maxspc; n++) { if ((distdone[n][m]!=1) && (nodefound[n]==1)) { distmat[n][m] = nodedist[n] + Ctree->ebrnchp[outgroup]->length; distmat[m][n] = distmat[n][m]; distdone[n][m] = 1; distdone[m][n] = 1; } /* if */ } /* for n */ free(nodefound); free(distdone); free(nodedist); } #endif /* SONJA */ /***************************************************************************/ /* end of SONJA */ /***************************************************************************/ /* write output file */ void writeoutputfile(FILE *ofp, int part) { int i, fail, df; uli li; double pval, delta; if ((part == WRITEPARAMS) || (part == WRITEALL)) { # ifndef ALPHA fprintf(ofp, "TREE-PUZZLE %s\n\n", VERSION); # else fprintf(ofp, "TREE-PUZZLE %s%s\n\n", VERSION, ALPHA); # endif fprintf(ofp, "Input file name: %s\n",INFILE); if (puzzlemode == USERTREE || puzzlemode == CONSENSUS) fprintf(ofp, "User tree file name: %s\n",INTREE); fprintf(ofp, "Type of analysis: "); switch(typ_optn) { case TREERECON_OPTN: switch(puzzlemode) { case CONSENSUS: fprintf(ofp, "consensus construction\n"); break; case USERTREE: fprintf(ofp, "user tree evaluation\n"); break; default: fprintf(ofp, "tree reconstruction\n"); break; } break; case LIKMAPING_OPTN: fprintf(ofp, "likelihood mapping\n"); break; } fprintf(ofp, "Parameter estimation: "); if (approxp_optn) fprintf(ofp, "approximate (faster)\n"); else fprintf(ofp, "accurate (slow)\n"); if (!((puzzlemode == USERTREE || puzzlemode == CONSENSUS) && typ_optn == TREERECON_OPTN)) { fprintf(ofp, "Parameter estimation uses: "); if (qcalg_optn) fprintf(ofp, "quartet sampling (for substitution process) + NJ tree (for rate variation)\n"); else fprintf(ofp, "neighbor-joining tree (for substitution process and rate variation)\n"); } else { fprintf(ofp, "Parameter estimation uses: "); if (utree_optn) fprintf(ofp, "1st user tree (for substitution process and rate variation)\n"); else if (qcalg_optn) fprintf(ofp, "quartet sampling (for substitution process) + NJ tree (for rate variation)\n"); else fprintf(ofp, "neighbor-joining tree (for substitution process and rate variation)\n"); } fprintf(ofp, "\nStandard errors (S.E.) are obtained by the curvature method.\n"); fprintf(ofp, "The upper and lower bounds of an approximate 95%% confidence interval\n"); fprintf(ofp, "for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E.\n"); fprintf(ofp, "\n\n"); /***************************************************************************/ /* SEQUENCE ALIGNMENT */ /***************************************************************************/ fprintf(ofp, "SEQUENCE ALIGNMENT\n\n"); #ifndef USE_WINDOWS fprintf(ofp, "Input data: %d sequences with %d ", Maxspc, Maxsite); #else fprintf(ofp, "Input data: %d sequences with %d ", Maxspc, alimaxsite); #endif if (data_optn == AMINOACID) fprintf(ofp, "amino acid"); else if (data_optn == NUCLEOTIDE && SH_optn) #ifndef USE_WINDOWS fprintf(ofp, "doublet (%d nucleotide)", Maxsite*2); #else fprintf(ofp, "doublet (%d nucleotide)", alimaxsite*2); #endif else if (data_optn == NUCLEOTIDE && nuc_optn) fprintf(ofp, "nucleotide"); else if (data_optn == BINARY) fprintf(ofp, "binary state"); fprintf(ofp, " sites"); if (data_optn == NUCLEOTIDE && (Maxseqc % 3) == 0 && !SH_optn) { if (codon_optn == 1) fprintf(ofp, " (1st codon positions)"); if (codon_optn == 2) fprintf(ofp, " (2nd codon positions)"); if (codon_optn == 3) fprintf(ofp, " (3rd codon positions)"); if (codon_optn == 4) fprintf(ofp, " (1st and 2nd codon positions)"); } if (data_optn == NUCLEOTIDE && SH_optn) { if (SHcodon) fprintf(ofp, " (1st and 2nd codon positions)"); else fprintf(ofp, " (1st+2nd, 3rd+4th, etc. site)"); } fprintf(ofp, "\n"); fprintf(ofp, "Number of constant sites: %d (= %.1f%% of all sites)\n", Numconst, 100.0*fracconst); fprintf(ofp, "Number of site patterns: %d\n", Numptrn); fprintf(ofp, "Number of constant site patterns: %d (= %.1f%% of all site patterns)\n\n\n", Numconstpat, 100.0*fracconstpat); /***************************************************************************/ /* SUBSTITUTION PROCESS */ /***************************************************************************/ fprintf(ofp, "SUBSTITUTION PROCESS\n\n"); fprintf(ofp, "Model of substitution: "); if (data_optn == NUCLEOTIDE) { /* nucleotides */ if (nuc_optn) { if(HKY_optn) fprintf(ofp, "HKY (Hasegawa et al. 1985)\n"); if(TN_optn) fprintf(ofp, "TN (Tamura-Nei 1993)\n"); if(GTR_optn) fprintf(ofp, "GTR (e.g. Lanave et al. 1980)\n"); if((HKY_optn) || (TN_optn)) { fprintf(ofp, "Transition/transversion parameter"); if (optim_optn) fprintf(ofp, " (estimated from data set)"); fprintf(ofp, ": %.2f", TSparam); if (optim_optn) fprintf(ofp, " (S.E. %.2f)", tserr); fprintf(ofp, "\n"); if (optim_optn && TSparam > MAXTS - 1.0) fprintf(ofp, "WARNING --- parameter estimate close to internal upper bound!\n"); if (optim_optn && TSparam < MINTS + 0.1) fprintf(ofp, "WARNING --- parameter estimate close to internal lower bound!\n"); } if (TN_optn) { fprintf(ofp, "Y/R transition parameter"); if (optim_optn) fprintf(ofp, " (estimated from data set)"); fprintf(ofp, ": %.2f", YRparam); if (optim_optn) fprintf(ofp, " (S.E. %.2f)", yrerr); fprintf(ofp, "\n"); if (optim_optn && YRparam > MAXYR - 0.5) fprintf(ofp, "WARNING --- parameter estimate close to internal upper bound!\n"); if (optim_optn && YRparam < MINYR + 0.1) fprintf(ofp, "WARNING --- parameter estimate close to internal lower bound!\n"); } if (GTR_optn || print_GTR_optn) { if((HKY_optn) || (TN_optn)) fprintf(ofp, "\n"); fprintf(ofp, "Rate matrix R (parameters %s):\n\n", GTR_optn ? "set by user" : "restricted to selected model"); fprintf(ofp, " A-C rate: "); fprintf(ofp, "%.5f\n", GTR_ACrate); fprintf(ofp, " A-G rate: "); fprintf(ofp, "%.5f\n", GTR_AGrate); fprintf(ofp, " A-T rate: "); fprintf(ofp, "%.5f\n", GTR_ATrate); fprintf(ofp, " C-G rate: "); fprintf(ofp, "%.5f\n", GTR_CGrate); fprintf(ofp, " C-T rate: "); fprintf(ofp, "%.5f\n", GTR_CTrate); fprintf(ofp, " G-T rate: "); fprintf(ofp, "%.5f\n", GTR_GTrate); fprintf(ofp, "\n"); } } if (SH_optn) { fprintf(ofp, "SH (Schoeniger-von Haeseler 1994)\n"); fprintf(ofp, "Transition/transversion parameter"); if (optim_optn) fprintf(ofp, " (estimated from data set)"); fprintf(ofp, ": %.2f\n", TSparam); if (optim_optn) fprintf(ofp, " (S.E. %.2f)", tserr); fprintf(ofp, "\n"); if (optim_optn && TSparam > MAXTS - 1.0) fprintf(ofp, "WARNING --- parameter estimate close to internal upper bound!\n"); if (optim_optn && TSparam < MINTS + 0.1) fprintf(ofp, "WARNING --- parameter estimate close to internal lower bound!\n"); } } if (data_optn == AMINOACID) { /* amino acids */ if (Dayhf_optn) fprintf(ofp, "Dayhoff (Dayhoff et al. 1978)\n"); if (Jtt_optn) fprintf(ofp, "JTT (Jones et al. 1992)\n"); if (mtrev_optn) fprintf(ofp, "mtREV24 (Adachi-Hasegawa 1996)\n"); if (cprev_optn) fprintf(ofp, "cpREV45 (Adachi et al. 2000)\n"); if (blosum62_optn) fprintf(ofp, "BLOSUM 62 (Henikoff-Henikoff 1992)\n"); if (vtmv_optn) fprintf(ofp, "VT (Mueller-Vingron 2000)\n"); if (wag_optn) fprintf(ofp, "WAG (Whelan-Goldman 2000)\n"); } if (data_optn == BINARY) { /* binary states */ fprintf(ofp, "Two-state model (Felsenstein 1981)\n"); } if (data_optn == AMINOACID) fprintf(ofp, "Amino acid "); else if (data_optn == NUCLEOTIDE && SH_optn) fprintf(ofp, "Doublet "); else if (data_optn == NUCLEOTIDE && nuc_optn) fprintf(ofp, "Nucleotide "); else if (data_optn == BINARY) fprintf(ofp, "Binary state "); fprintf(ofp, "frequencies ("); if (Frequ_optn) fprintf(ofp, "estimated from data set"); else fprintf(ofp, "user specified"); if (data_optn == NUCLEOTIDE && SH_optn && sym_optn) fprintf(ofp, " and symmetrized"); fprintf(ofp, "):\n\n"); for (i = 0; i < gettpmradix(); i++) fprintf(ofp, " pi(%s) = %5.1f%%\n", int2code(i), Freqtpm[i]*100); if (data_optn == NUCLEOTIDE) { if (!GTR_optn) { fprintf(ofp, "\nExpected transition/transversion ratio: %.2f", tstvratio); if (tstvf84 == 0.0) fprintf(ofp, "\n"); else fprintf(ofp, " (= F84 parameter)\n"); fprintf(ofp, "Expected pyrimidine transition/purine transition"); fprintf(ofp, " ratio: %.2f\n", yrtsratio); if (tstvf84 != 0.0 && TN_optn) fprintf(ofp, "This TN model is equivalent to a F84 model (Felsenstein 1984).\n"); } } /***************************************************************************/ /* SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) */ /***************************************************************************/ fprintf(ofp, "\n\nAMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER)\n\n"); { double fract; int sumgapchar=0; int sumotherchar=0; fprintf(ofp, " gaps wildcards sum %% sequence\n"); for (i = 0; i < Maxspc; i++) { fprintf(ofp, " "); fputid10(ofp, i); fprintf(ofp, " "); #ifndef USE_WINDOWS fract = (Seqgapchar[i] + Seqotherchar[i]) / (double) Maxsite; #else fract = (Seqgapchar[i] + Seqotherchar[i]) / (double) alimaxsite; #endif sumgapchar+=Seqgapchar[i]; sumotherchar+=Seqotherchar[i]; fprintf(ofp, "%6d %6d %6d %6.2f%% %c\n", Seqgapchar[i], Seqotherchar[i], (Seqgapchar[i] + Seqotherchar[i]), 100.0 * fract, ((fract > 0.5) ? '!' : ' ')); } fprintf(ofp, " -------------------------------------------------------\n"); fprintf(ofp, " Sum "); #ifndef USE_WINDOWS fract = (sumgapchar + sumotherchar) / (double) (Maxsite * Maxspc); #else fract = (sumgapchar + sumotherchar) / (double) (alimaxsite * Maxspc); #endif fprintf(ofp, "%6d %6d %6d %6.2f%% %c\n", sumgapchar, sumotherchar, (sumgapchar + sumotherchar), 100.0 * fract, ((fract > 0.5) ? '!' : ' ')); fprintf(ofp, "\n\n"); fprintf(ofp, "The table above shows the amount of gaps ('-') and other 'wildcard'\n"); #ifndef USE_WINDOWS fprintf(ofp, "characters ('X', '?', etc.) and their percentage of the %d columns\n", Maxsite); #else fprintf(ofp, "characters ('X', '?', etc.) and their percentage of the %d columns\n", alimaxsite); #endif fprintf(ofp, "in the alignment.\n"); fprintf(ofp, "Sequences with more than 50%% ambiguous characters are marked with a '!' and \n"); fprintf(ofp, "should be checked, whether they have sufficient overlap to other sequences.\n"); fprintf(ofp, "Sequences with 100%% ambiguous characters do not hold any phylogenetic\n"); fprintf(ofp, "information and had to be discarded from the analysis.\n\n"); } /***************************************************************************/ /* SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) */ /***************************************************************************/ fprintf(ofp, "\n\nSEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER)\n\n"); fail = FALSE; fprintf(ofp, " 5%% chi-square test p-value\n"); for (i = 0; i < Maxspc; i++) { fprintf(ofp, " "); fputid10(ofp, i); pval = homogentest(i); if ( pval < 0.05 ) fprintf(ofp, " failed "); else fprintf(ofp, " passed "); if (chi2fail) fail = TRUE; fprintf(ofp, " %6.2f%% ", pval*100.0); fprintf(ofp, "\n"); } fprintf(ofp, "\n"); fprintf(ofp, "The chi-square tests compares the "); if (data_optn == AMINOACID) fprintf(ofp, "amino acid"); else if (data_optn == NUCLEOTIDE && SH_optn) fprintf(ofp, "doublet"); else if (data_optn == NUCLEOTIDE && nuc_optn) fprintf(ofp, "nucleotide"); else if (data_optn == BINARY) fprintf(ofp, "binary state"); fprintf(ofp," composition of each sequence\n"); fprintf(ofp, "to the frequency distribution assumed in the maximum likelihood model.\n"); if (fail) { fprintf(ofp, "\nWARNING: Result of chi-square test may not be valid"); fprintf(ofp, " because of small\nmaximum likelihood frequencies and"); fprintf(ofp, " short sequence length!\n"); } /***************************************************************************/ /* IDENTICAL SEQUENCE */ /***************************************************************************/ fprintf(ofp, "\n\nIDENTICAL SEQUENCES\n\n"); fprintf(ofp, "The sequences in each of the following groups are all identical. To speed\n"); fprintf(ofp, "up computation please remove all but one of each group from the data set.\n\n"); findidenticals(ofp); fprintf(ofp, "\n\nMAXIMUM LIKELIHOOD DISTANCES\n\n"); fprintf(ofp, "Maximum likelihood distances are computed using the "); fprintf(ofp, "selected model of\nsubstitution and rate heterogeneity.\n\n"); putdistance(ofp); { double avgdist, meandist, mindist, maxdist, stddevdist, vardist; avgdist = averagedist(Maxspc, Distanmat, &meandist, &mindist, &maxdist, &stddevdist, &vardist); fprintf(ofp, "\nAverage distance (over all possible pairs of sequences): %.5f\n", meandist); fprintf(ofp, " minimum : %.5f, maximum : %.5f\n", mindist, maxdist); fprintf(ofp, " variance : %.5f, std.dev. : %.5f\n", vardist, stddevdist); } /***************************************************************************/ /* RATE HETEROGENEITY (PART 1) */ /***************************************************************************/ fprintf(ofp, "\n\nRATE HETEROGENEITY\n\n"); fprintf(ofp, "Model of rate heterogeneity: "); if (rhetmode == UNIFORMRATE) fprintf(ofp, "uniform rate\n"); if (rhetmode == GAMMARATE ) fprintf(ofp, "Gamma distributed rates\n"); if (rhetmode == TWORATE ) fprintf(ofp, "two rates (1 invariable + 1 variable)\n"); if (rhetmode == MIXEDRATE ) fprintf(ofp, "mixed (1 invariable + %d Gamma rates)\n", numcats); if (rhetmode == TWORATE || rhetmode == MIXEDRATE) { fprintf(ofp, "Fraction of invariable sites"); if (fracinv_optim) fprintf(ofp, " (estimated from data set)"); fprintf(ofp, ": %.2f", fracinv); if (fracinv_optim) fprintf(ofp, " (S.E. %.2f)", fierr); fprintf(ofp, "\n"); if (fracinv_optim && fracinv > MAXFI - 0.05) fprintf(ofp, "WARNING --- parameter estimate close to internal upper bound!\n"); #ifndef USE_WINDOWS fprintf(ofp, "Number of invariable sites: %.0f\n", floor(fracinv*Maxsite)); #else fprintf(ofp, "Number of invariable sites: %.0f\n", floor(fracinv*alimaxsite)); #endif } if (rhetmode == GAMMARATE || rhetmode == MIXEDRATE) { fprintf(ofp, "Gamma distribution parameter alpha"); if (grate_optim) fprintf(ofp, " (estimated from data set)"); fprintf(ofp, ": %.2f", (1.0-Geta)/Geta); if (grate_optim) fprintf(ofp, " (S.E. %.2f)", geerr/(Geta*Geta)); /* first order approximation */ fprintf(ofp, "\n"); if (grate_optim && Geta > MAXGE - 0.02) fprintf(ofp, "WARNING --- parameter estimate close to internal upper bound!\n"); if (grate_optim && Geta < MINGE + 0.01) fprintf(ofp, "WARNING --- parameter estimate close to internal lower bound!\n"); fprintf(ofp, "Number of Gamma rate categories: %d\n", numcats); } if (rhetmode == MIXEDRATE) { fprintf(ofp, "Total rate heterogeneity (invariable sites + Gamma model): "); fprintf(ofp, "%.2f", fracinv + Geta - fracinv*Geta); if (grate_optim && fracinv_optim) fprintf(ofp, " (S.E. %.2f)", geerr + fierr); /* first order approximation */ else if (grate_optim && !fracinv_optim) fprintf(ofp, " (S.E. %.2f)", geerr); else if (!grate_optim && fracinv_optim) fprintf(ofp, " (S.E. %.2f)", fierr); fprintf(ofp, "\n"); } if (rhetmode != UNIFORMRATE) { fprintf(ofp, "\nRates and their respective probabilities used in the likelihood function:\n"); fprintf(ofp, "\n Category Relative rate Probability\n"); if (rhetmode == TWORATE || rhetmode == MIXEDRATE) fprintf(ofp, " 0 0.0000 %.4f\n", fracinv); for (i = 0; i < numcats; i++) fprintf(ofp, " %d %.4f %.4f\n", i+1, Rates[i], (1.0-fracinv)/(double) numcats); } if (rhetmode == GAMMARATE || rhetmode == MIXEDRATE) { fprintf(ofp, "\nCategories 1-%d approximate a continous ", numcats); fprintf(ofp, "Gamma-distribution with expectation 1\n"); fprintf(ofp, "and variance "); if (Geta == 1.0) fprintf(ofp, "infinity"); else fprintf(ofp, "%.2f", Geta/(1.0-Geta)); fprintf(ofp, ".\n"); } } /* if WRITEPARAMS) || WRITEALL */ if ((part == WRITEREST) || (part == WRITEALL)) { /***************************************************************************/ /* RATE HETEROGENEITY (PART 2) */ /***************************************************************************/ #if 0 if (typ_optn == TREERECON_OPTN && (puzzlemode == QUARTPUZ || puzzlemode == USERTREE || puzzlemode == CONSENSUS) && !skipmlbranch_optn) { #endif #if 0 if(typ_optn == TREERECON_OPTN) fprintf(stderr, "typ_optn == TREERECON_OPTN\n"); if(puzzlemode == QUARTPUZ) fprintf(stderr, "puzzlemode == QUARTPUZZ\n"); if(puzzlemode == USERTREE) fprintf(stderr, "puzzlemode == USERTREE\n"); if(puzzlemode == CONSENSUS) fprintf(stderr, "puzzlemode == CONSENSUS\n"); if(dotreelh_optn) fprintf(stderr, "dotreelh_optn\n"); #endif if (typ_optn == TREERECON_OPTN && (puzzlemode == QUARTPUZ || puzzlemode == USERTREE || puzzlemode == CONSENSUS) && dotreelh_optn) { /* if likelihood has been computed */ if (rhetmode != UNIFORMRATE) { fprintf(ofp, "\nCombination of categories that contributes"); fprintf(ofp, " the most to the likelihood\n"); fprintf(ofp, "(computation done without clock assumption assuming "); if (puzzlemode == QUARTPUZ) fprintf(ofp, "quartet-puzzling tree"); if (puzzlemode == USERTREE || puzzlemode == CONSENSUS) { if (utree_optn) fprintf(ofp, "1st user tree"); else fprintf(ofp, "NJ tree"); } fprintf(ofp, "):\n\n"); if (bestratefound==0) { fprintf(STDOUT, "ERROR: no rate combination computed before output!!!\n"); findbestratecombination(); } printbestratecombination(ofp); } /* rhetmode != UNIFORMRATE */ if (savesiterate_optn) { FILE *ratefp; openfiletowrite(&ratefp, SITERATE, "site rates"); printbestratecombinationtofile(ratefp, rhetmode); fclose(ratefp); } /* if savesiterate_optn */ } /* if likelihood has been computed */ /***************************************************************************/ /* BAD QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) */ /***************************************************************************/ if (puzzlemode == QUARTPUZ &&typ_optn == TREERECON_OPTN) { fprintf(ofp, "\n\nQUARTET STATISTICS (SEQUENCES IN INPUT ORDER)\n\n"); fprintf(ofp, "\n"); fprintf(ofp, " name | resolved | partly resolved | unresolved | sum\n"); fprintf(ofp, " --------------------------------------------------------------------------\n"); for (i = 0; i < Maxspc; i++) { /* fprintf(ofp, " %3d. %-10s %6.2f%% [%7ld] %6.2f%% [%7ld] %6.2f%% [%7ld] %7ld\n", */ /* fprintf(ofp, " %3d. %-10s (%6.2f%%) %7ld (%6.2f%%) %7ld (%6.2f%%) %7ld %7ld\n", */ fprintf(ofp, " %-10s %7ld [%6.2f%%] %7ld [%6.2f%%] %7ld [%6.2f%%] %7ld\n", Namestr[i], (qinfomatr[1][i]+qinfomatr[2][i]+qinfomatr[4][i]), (100.0 * (qinfomatr[1][i]+qinfomatr[2][i]+qinfomatr[4][i])/qinfomatr[8][i]), (qinfomatr[3][i]+qinfomatr[5][i]+qinfomatr[6][i]), (100.0 * (qinfomatr[3][i]+qinfomatr[5][i]+qinfomatr[6][i])/qinfomatr[8][i]), qinfomatr[7][i], (100.0 * (qinfomatr[7][i])/qinfomatr[8][i]), qinfomatr[8][i]); /* MISSING QUARTETS (HAS ;-) */ } fprintf(ofp, " --------------------------------------------------------------------------\n"); fprintf(ofp, " #quartets :"); { uli allqs; allqs = fullresqs + partresqs + unresqs + missingqs; fprintf(ofp, "%7ld [%6.2f%%] ", fullresqs, 100.0 * fullresqs / allqs); fprintf(ofp, "%7ld [%6.2f%%] ", partresqs, 100.0 * partresqs / allqs); fprintf(ofp, "%7ld [%6.2f%%] ", unresqs, 100.0 * unresqs / allqs); /* MISSING QUARTETS (HAS ;-) */ /* fprintf(ofp, "%7ld [%6.2f%%] ", missingqs, 100.0 * missingqs / allqs); */ fprintf(ofp, "%7ld", allqs); } fprintf(ofp, "\n\n"); fprintf(ofp, "The table shows the occurrences of fully resolved, partially, and\n"); fprintf(ofp, "completely unresolved quartets for each sequence and their percentage\n"); fprintf(ofp, "relative to the number of times the sequence occurs in the list of \n"); fprintf(ofp, "quartets (i.e. %ld quartets out of %ld in total).\n", (4 * Numquartets)/Maxspc, Numquartets); fprintf(ofp, "In fully resolved quartet one single topology is supported, while for\n"); fprintf(ofp, "partially resolved quartets two and for completely unresolved quartets\n"); fprintf(ofp, "none of the topologies (AB||CD, AC||BD, AD||BC) are favoured.\n"); fprintf(ofp, "Note: Because 4 sequences are involved in one quartet numbers add up\n"); fprintf(ofp, "to a four-fold of the existing quartets.\n"); fprintf(ofp, "\n"); fprintf(ofp, "Hint: The overall numbers in the last row give information about the\n"); fprintf(ofp, "phylogenetic content of the dataset. The higher the percentage of partially\n"); fprintf(ofp, "and unresolved quartets, the lower the content of phylogenetic information.\n"); fprintf(ofp, "This can be visualized in more detail by likelihood mapping analysis.\n"); fprintf(ofp, "\n"); } if (typ_optn == TREERECON_OPTN) { /***************************************************************************/ /* TREE SEARCH */ /***************************************************************************/ fprintf(ofp, "\n\nTREE SEARCH\n\n"); if (puzzlemode == QUARTPUZ) { fprintf(ofp, "Quartet puzzling is used to choose from the possible tree topologies\n"); fprintf(ofp, "and to simultaneously infer support values for internal branches.\n\n"); fprintf(ofp, "Number of puzzling steps: %lu\n", Numtrial); fprintf(ofp, "Analysed quartets: %lu\n", Numquartets); fprintf(ofp, "Fully resolved quartets: %lu (= %.1f%%)\n", fullresqs, (double) fullresqs / (double) Numquartets * 100.0); fprintf(ofp, "Partly resolved quartets: %lu (= %.1f%%)\n", partresqs, (double) partresqs / (double) Numquartets * 100.0); fprintf(ofp, "Unresolved quartets: %lu (= %.1f%%)\n", unresqs, (double) unresqs / (double) Numquartets * 100.0); /* MISSING QUARTETS (HAS ;-) */ /* fprintf(ofp, "Missing quartets: %lu (= %.1f%%)\n", missingqs, (double) missingqs / (double) Numquartets * 100.0); */ fprintf(ofp, "\nQuartet trees are based on %s maximum likelihood values\n", (approxqp ? "approximate" : "exact")); fprintf(ofp, "using the selected model of substitution and rate heterogeneity.\n"); } if (puzzlemode == USERTREE || puzzlemode == CONSENSUS) { fprintf(ofp, "%d tree topologies were specified by the user.\n", numutrees); } if (puzzlemode == PAIRDIST) { fprintf(ofp, "No tree search performed (maximum likelihood distances only).\n"); } /***************************************************************************/ /* QUARTET PUZZLING TREE / CONSENSUS TREE */ /***************************************************************************/ if ((puzzlemode == QUARTPUZ) || (puzzlemode == CONSENSUS)) { if (puzzlemode == QUARTPUZ) { fprintf(ofp, "\n\nQUARTET PUZZLING TREE\n\n"); fprintf(ofp, "Support for the internal branches of the unrooted quartet puzzling\n"); fprintf(ofp, "tree topology is shown in percent.\n"); if (consincluded == (Maxspc - 3)) fprintf(ofp,"\nThis quartet puzzling tree is completely resolved.\n"); else fprintf(ofp,"\nThis quartet puzzling tree is not completely resolved!\n"); } else { fprintf(ofp, "\n\nCONSENSUS TREE\n\n"); fprintf(ofp, "Support for the internal branches of the unrooted consensus tree\n"); fprintf(ofp, "topology is shown in percent.\n"); if (consincluded == (Maxspc - 3)) fprintf(ofp,"\nThis consensus tree is completely resolved.\n"); else fprintf(ofp,"\nThis consensus tree is not completely resolved!\n"); } fprintf(ofp, "\n\n"); plotconsensustree(ofp); if (puzzlemode == QUARTPUZ) fprintf(ofp, "\n\nQuartet puzzling tree (in CLUSTAL W notation):\n\n"); else fprintf(ofp, "\n\nConsensus tree (in CLUSTAL W notation):\n\n"); writeconsensustree(ofp, FALSE, qsupportarr); if (qsupport_optn) writeconsensustree(ofp, TRUE, qsupportarr); if (puzzlemode == QUARTPUZ) { fprintf(ofp, "\n\nBIPARTITIONS\n\n"); fprintf(ofp, "The following bipartitions occured at least once"); fprintf(ofp, " in all intermediate\ntrees that have been generated "); fprintf(ofp, "in the %lu puzzling steps.\n", Numtrial); fprintf(ofp, "Bipartitions included in the quartet puzzling tree:\n"); } else { fprintf(ofp, "\n\nBIPARTITIONS\n\n"); fprintf(ofp, "The following bipartitions occured at least once"); fprintf(ofp, " in the specified set\n of %d usertrees tree topologies.\n", numutrees); fprintf(ofp, "Bipartitions included in the consensus tree:\n"); } fprintf(ofp, "(bipartition with sequences in input order : number of times seen)\n\n"); for (li = 0; li < (uli)consfifty; li++) { fprintf(ofp, " "); fprintfsplit(ofp, splitfreqs[2*li+1], splitpatterns, splitlength, Maxspc); fprintf(ofp, " : %lu", splitfreqs[2*li]); /* MISSING QUARTETS (HAS ;-) */ /* todo (HAS) */ if (qsupport_optn) { fprintf(ofp, " f+=%.0f|", (100.0*qsupportarr[li].fullres_pro/qsupportarr[li].qsum)); fprintf(ofp, "p+=%.0f|", (100.0*qsupportarr[li].partres_pro/qsupportarr[li].qsum)); fprintf(ofp, "f-=%.0f|", (100.0*qsupportarr[li].fullres_con/qsupportarr[li].qsum)); fprintf(ofp, "p-=%.0f|", (100.0*qsupportarr[li].partres_con/qsupportarr[li].qsum)); fprintf(ofp, "ur=%.0f", (100.0*qsupportarr[li].unres/qsupportarr[li].qsum)); if (qsupportarr[li].missing > 0) { fprintf(ofp, "|md=%.0f", (100.0*qsupportarr[li].missing/qsupportarr[li].qsum)); } fprintf(ofp, "/%ld\n", qsupportarr[li].qsum); } else { fprintf(ofp, "\n"); } #if 0 #endif } if (consincluded == 0) fprintf(ofp, " None (no bipartition included)\n"); if (conssub50_optn) { if (! puzzlemode == CONSENSUS) fprintf(ofp, "\nCongruent bipartitions occurred in 50%% or less, included in \nthe quartet puzzling tree:\n"); else fprintf(ofp, "\nCongruent bipartitions occurred in 50%% or less, included in \nthe consensus tree:\n"); } else { if (! puzzlemode == CONSENSUS) fprintf(ofp, "\nCongruent bipartitions occurred in 50%% or less, not included in \nthe quartet puzzling tree:\n"); else fprintf(ofp, "\nCongruent bipartitions occurred in 50%% or less, not included in \nthe consensus tree:\n"); } fprintf(ofp, "(bipartition with sequences in input order : number of times seen)\n\n"); if ((uli)consfifty == numbiparts) { fprintf(ofp, " None (all bipartitions are included)\n"); } else { if (consfifty < conscongruent) { for (li = (uli)consfifty; (li < (uli)numbiparts) && (li < (uli)conscongruent); li++) { fprintf(ofp, " "); fprintfsplit(ofp, splitfreqs[2*li+1], splitpatterns, splitlength, Maxspc); fprintf(ofp, " : %lu", splitfreqs[2*li]); /* MISSING QUARTETS (HAS ;-) */ /* todo (HAS) */ if (qsupport_optn) { fprintf(ofp, "f+=%.0f|", (100.0*qsupportarr[li].fullres_pro/qsupportarr[li].qsum)); fprintf(ofp, "p+=%.0f|", (100.0*qsupportarr[li].partres_pro/qsupportarr[li].qsum)); fprintf(ofp, "f-=%.0f|", (100.0*qsupportarr[li].fullres_con/qsupportarr[li].qsum)); fprintf(ofp, "p-=%.0f|", (100.0*qsupportarr[li].partres_con/qsupportarr[li].qsum)); fprintf(ofp, "ur=%.0f", (100.0*qsupportarr[li].unres/qsupportarr[li].qsum)); if (qsupportarr[li].missing > 0) { fprintf(ofp, "|md=%.0f", (100.0*qsupportarr[li].missing/qsupportarr[li].qsum)); } fprintf(ofp, "/%ld\n", qsupportarr[li].qsum); } else { fprintf(ofp, "\n"); } #if 0 #endif } } else { fprintf(ofp, " None (No congruent split not included)\n"); } if (! puzzlemode == CONSENSUS) fprintf(ofp, "\nIncongruent bipartitions not included in the quartet puzzling tree:\n"); else fprintf(ofp, "\nIncongruent bipartitions not included in the consensus tree:\n"); fprintf(ofp, "(bipartition with sequences in input order : number of times seen)\n\n"); /* print next 20 bipartions not included */ for (li = conscongruent; (li < numbiparts) && (li < conscongruent + 20UL); li++) { fprintf(ofp, " "); fprintfsplit(ofp, splitfreqs[2*li+1], splitpatterns, splitlength, Maxspc); fprintf(ofp, " : %lu\n", splitfreqs[2*li]); } if ((li == conscongruent + 20UL) && (li != numbiparts)) fprintf(ofp, "\n(%lu other less frequent bipartitions not shown)\n", numbiparts - conscongruent - 20UL); } if (! puzzlemode == CONSENSUS) { fprintfsortedpstrees(ofp, psteptreelist, psteptreenum, psteptreesum, 0, 5.0); } } /***************************************************************************/ /* MAXIMUM LIKELIHOOD BRANCH LENGTHS ON QUARTET PUZZLING TREE (NO CLOCK) */ /***************************************************************************/ #if 0 if (((puzzlemode == QUARTPUZ) || (puzzlemode == CONSENSUS)) && !skipmlbranch_optn) { #endif if (((puzzlemode == QUARTPUZ) || (puzzlemode == CONSENSUS)) && dotreelh_optn) { if (! puzzlemode == CONSENSUS) { fprintf(ofp, "\n\nMAXIMUM LIKELIHOOD BRANCH LENGTHS ON QUARTET"); fprintf(ofp, " PUZZLING TREE (NO CLOCK)\n\nBranch lengths are computed using"); fprintf(ofp, " the selected model of\nsubstitution and rate heterogeneity.\n\n\n"); } else { fprintf(ofp, "\n\nMAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS"); fprintf(ofp, " TREE (NO CLOCK)\n\nBranch lengths are computed using"); fprintf(ofp, " the selected model of\nsubstitution and rate heterogeneity.\n\n\n"); } clockmode = 0; /* nonclocklike branch lengths */ prtopology(ofp); fprintf(ofp, "\n"); resulttree(ofp, FALSE); /* branch lengths cannot be set by user in this case */ if (! puzzlemode == CONSENSUS) { fprintf(ofp, "\n\nQuartet puzzling tree with maximum likelihood branch lengths"); fprintf(ofp, "\n(in CLUSTAL W notation):\n\n"); } else { fprintf(ofp, "\n\nConsensus tree with maximum likelihood branch lengths"); fprintf(ofp, "\n(in CLUSTAL W notation):\n\n"); } fputphylogeny(ofp); /* SONJA */ #ifdef SONJA /* computes the distances in the tree and writes them to file/stderr */ tree2dist(Distanmat); putdistance(ofp); putdistance(stderr); #endif /*****************************************************************************/ /* MAXIMUM LIKELIHOOD BRANCH LENGTHS ON QUARTET PUZZLING TREE (WITH CLOCK) */ /*****************************************************************************/ if (compclock) { if (! puzzlemode == CONSENSUS) { fprintf(ofp, "\n\nMAXIMUM LIKELIHOOD BRANCH LENGTHS OF QUARTET"); fprintf(ofp, " PUZZLING TREE (WITH CLOCK)\n\nBranch lengths are computed using"); } else { fprintf(ofp, "\n\nMAXIMUM LIKELIHOOD BRANCH LENGTHS OF CONSENSUS"); fprintf(ofp, " TREE (WITH CLOCK)\n\nBranch lengths are computed using"); } fprintf(ofp, " the selected model of\nsubstitution and rate heterogeneity.\n"); fprintf(ofp, "\nRoot located at branch: %d ", locroot+1); if (locroot 1) fprintf(ofp, "- WARNING: %d best locations found! -", numbestroot); fprintf(ofp, "\n\n"); fprintf(ofp, "If the automatic search misplaces the root please rerun the analysis\n"); fprintf(ofp, "(rename \"outtree\" to \"intree\") and select location of root manually!"); fprintf(ofp, "\n\n\n"); } if (rootsearch == ROOT_DISPLAYED) fprintf(ofp, "(displayed outgroup)\n\n\n"); clockmode = 1; /* clocklike branch lengths */ prtopology(ofp); fprintf(ofp, "\n"); fprintf(ofp, "\nTree drawn as unrooted tree for better "); fprintf(ofp, "comparison with non-clock tree!\n"); resulttree(ofp, usebranch_optn); fprintf(ofp, "\n"); resultheights(ofp); if (! puzzlemode == CONSENSUS) { fprintf(ofp, "\n\nRooted quartet puzzling tree with clocklike"); } else { fprintf(ofp, "\n\nRooted consensus tree with clocklike"); } fprintf(ofp, " maximum likelihood branch lengths\n"); fprintf(ofp, "(in CLUSTAL W notation):\n\n"); fputrooted(ofp, locroot); } /***************************************************************************/ /* MOLECULAR CLOCK LIKELIHOOD RATIO TEST */ /***************************************************************************/ if (compclock) { fprintf(ofp, "\n\nMOLECULAR CLOCK LIKELIHOOD RATIO TEST\n\n"); fprintf(ofp, "log L without clock: %.2f (independent branch parameters: %d)\n", Ctree->lklhd, Numspc + Numibrnch); fprintf(ofp, "log L with clock: %.2f (independent branch parameters: %d)\n\n", Ctree->lklhdc, Numhts + 1); delta = fabs(2.0*((Ctree->lklhd) - (Ctree->lklhdc))); fprintf(ofp, "Likelihood ratio test statistic delta: %.2f\n", delta); df = Numspc + Numibrnch - Numhts - 1; fprintf(ofp, "Degress of freedom of chi-square distribution: %d\n", df); pval = IncompleteGammaQ(df*0.5, delta*0.5); fprintf(ofp, "Critical significance level: %.2f%%\n\n", pval*100.0); if (pval >= 0.05) { fprintf(ofp, "The simpler (clocklike) tree can not be rejected on a significance\n"); fprintf(ofp, "level of 5%%. The log-likelihood of the more complex (no clock) tree\n"); fprintf(ofp, "is not significantly increased.\n"); } else { fprintf(ofp, "The simpler (clocklike) tree is rejected on a significance level\n"); fprintf(ofp, "of 5%%. The log-likelihood of the more complex (no clock) tree is\n"); fprintf(ofp, "significantly increased.\n"); } fprintf(ofp, "\nPlease take care that the correct root is used!\n"); } } } /***************************************************************************/ /* LIKELIHOOD MAPPING ANALYSIS */ /***************************************************************************/ if (typ_optn == LIKMAPING_OPTN) { fprintf(ofp, "\n\nLIKELIHOOD MAPPING ANALYSIS\n\n"); fprintf(ofp, "Number of quartets: %lu", Numquartets); if (lmqts == 0) fprintf(ofp, " (all possible)\n"); else fprintf(ofp, " (random choice)\n"); fprintf(ofp, "\nQuartet trees are based on approximate maximum likelihood values\n"); fprintf(ofp, "using the selected model of substitution and rate heterogeneity.\n\n\n"); if (numclust == 1) { fprintf(ofp, "Sequences are not grouped in clusters.\n"); } else { fprintf(ofp, "Sequences are grouped in %d clusters.\n", numclust); fprintf(ofp, "\nCluster a: %d sequences\n\n", clustA); for (i = 0; i < clustA; i++) { fprintf(ofp, " "); fputid(ofp, clusterA[i]); fprintf(ofp, "\n"); } fprintf(ofp, "\nCluster b: %d sequences\n\n", clustB); for (i = 0; i < clustB; i++) { fprintf(ofp, " "); fputid(ofp, clusterB[i]); fprintf(ofp, "\n"); } if (numclust > 2) { fprintf(ofp, "\nCluster c: %d sequences\n\n", clustC); for (i = 0; i < clustC; i++) { fprintf(ofp, " "); fputid(ofp, clusterC[i]); fprintf(ofp, "\n"); } } if (numclust == 4) { fprintf(ofp, "\nCluster d: %d sequences\n\n", clustD); for (i = 0; i < clustD; i++) { fprintf(ofp, " "); fputid(ofp, clusterD[i]); fprintf(ofp, "\n"); } } fprintf(ofp, "\nQuartets of sequences used in the likelihood"); fprintf(ofp, " mapping analysis are generated\n"); if (numclust == 2) fprintf(ofp, "by drawing two sequences from cluster a and two from cluster b."); if (numclust == 3) fprintf(ofp, "by drawing one sequence from clusters a and b and two from cluster c."); if (numclust == 4) fprintf(ofp, "by drawing one sequence from each of the clusters a, b, c, and d."); } /***************************************************************************/ /* LIKELIHOOD MAPPING STATISTICS */ /***************************************************************************/ fprintf(ofp, "\n\nLIKELIHOOD MAPPING STATISTICS\n\n"); fprintf(ofp, "Occupancies of the three areas 1, 2, 3:\n\n"); if (numclust == 4) fprintf(ofp, " (a,b)-(c,d)\n"); if (numclust == 3) fprintf(ofp, " (a,b)-(c,c)\n"); if (numclust == 2) fprintf(ofp, " (a,a)-(b,b)\n"); fprintf(ofp, " /\\\n"); fprintf(ofp, " / \\\n"); fprintf(ofp, " / \\\n"); fprintf(ofp, " / 1 \\\n"); fprintf(ofp, " / \\ / \\\n"); fprintf(ofp, " / \\ / \\\n"); fprintf(ofp, " / \\/ \\\n"); fprintf(ofp, " / 3 : 2 \\\n"); fprintf(ofp, " / : \\\n"); fprintf(ofp, " /__________________\\\n"); if (numclust == 4) fprintf(ofp, " (a,d)-(b,c) (a,c)-(b,d)\n"); if (numclust == 3) fprintf(ofp, " (a,c)-(b,c) (a,c)-(b,c)\n"); if (numclust == 2) fprintf(ofp, " (a,b)-(a,b) (a,b)-(a,b)\n"); fprintf(ofp, "\n"); fprintf(ofp, "Number of quartets in region 1: %lu (= %.1f%%)\n", ar1, (double) ar1*100.0/Numquartets); fprintf(ofp, "Number of quartets in region 2: %lu (= %.1f%%)\n", ar2, (double) ar2*100.0/Numquartets); fprintf(ofp, "Number of quartets in region 3: %lu (= %.1f%%)\n\n", ar3, (double) ar3*100.0/Numquartets); fprintf(ofp, "Occupancies of the seven areas 1, 2, 3, 4, 5, 6, 7:\n\n"); if (numclust == 4) fprintf(ofp, " (a,b)-(c,d)\n"); if (numclust == 3) fprintf(ofp, " (a,b)-(c,c)\n"); if (numclust == 2) fprintf(ofp, " (a,a)-(b,b)\n"); fprintf(ofp, " /\\\n"); fprintf(ofp, " / \\\n"); fprintf(ofp, " / 1 \\\n"); fprintf(ofp, " / \\ / \\\n"); fprintf(ofp, " / /\\ \\\n"); fprintf(ofp, " / 6 / \\ 4 \\\n"); fprintf(ofp, " / / 7 \\ \\\n"); fprintf(ofp, " / \\ /______\\ / \\\n"); fprintf(ofp, " / 3 : 5 : 2 \\\n"); fprintf(ofp, " /__________________\\\n"); if (numclust == 4) fprintf(ofp, " (a,d)-(b,c) (a,c)-(b,d)\n"); if (numclust == 3) fprintf(ofp, " (a,c)-(b,c) (a,c)-(b,c)\n"); if (numclust == 2) fprintf(ofp, " (a,b)-(a,b) (a,b)-(a,b)\n"); fprintf(ofp, "\n"); fprintf(ofp, "Number of quartets in region 1: %lu (= %.1f%%) left: %lu right: %lu\n", reg1, (double) reg1*100.0/Numquartets, reg1l, reg1r); fprintf(ofp, "Number of quartets in region 2: %lu (= %.1f%%) bottom: %lu top: %lu\n", reg2, (double) reg2*100.0/Numquartets, reg2d, reg2u); fprintf(ofp, "Number of quartets in region 3: %lu (= %.1f%%) bottom: %lu top: %lu\n", reg3, (double) reg3*100.0/Numquartets, reg3d, reg3u); fprintf(ofp, "Number of quartets in region 4: %lu (= %.1f%%) bottom: %lu top: %lu\n", reg4, (double) reg4*100.0/Numquartets, reg4d, reg4u); fprintf(ofp, "Number of quartets in region 5: %lu (= %.1f%%) left: %lu right: %lu\n", reg5, (double) reg5*100.0/Numquartets, reg5l, reg5r); fprintf(ofp, "Number of quartets in region 6: %lu (= %.1f%%) bottom: %lu top: %lu\n", reg6, (double) reg6*100.0/Numquartets, reg6d, reg6u); fprintf(ofp, "Number of quartets in region 7: %lu (= %.1f%%)\n", reg7, (double) reg7*100.0/Numquartets); } } /* if WRITEREST) || WRITEALL */ } /* writeoutputfile */ #if PARALLEL void writetimesstat(FILE *ofp) { int n; double cpusum = 0.0; double wallmax = 0.0; cputimes[0] = ((double)(cputimestop - cputimestart) / CLOCKS_PER_SEC); walltimes[0] = difftime(walltimestop, walltimestart); fullcpu = tarr.fullcpu; fulltime = tarr.fulltime; fullcputimes[0] = tarr.fullcpu; fullwalltimes[0] = tarr.fulltime; altcputimes[0] = tarr.cpu; altwalltimes[0] = tarr.time; fprintf(ofp, "\n\n\nPARALLEL LOAD STATISTICS\n\n"); fprintf(ofp, "The analysis was performed with %d parallel processes (1 master and \n", PP_NumProcs); fprintf(ofp, "%d worker processes).\n\n", PP_NumProcs-1); fprintf(ofp, "The following table the distribution of computation to the processes.\n"); fprintf(ofp, "The first column gives the process number, where 0 is the master process.\n"); fprintf(ofp, "The second and third column show the number of quartets computed (3 topologies \n"); fprintf(ofp, "each) and the the number of scheduling blocks the came in. The last two columns \n"); fprintf(ofp, "state the number of puzzling steps done by a process and number of scheduling \n"); fprintf(ofp, "blocks.\n\n"); fprintf(ofp, "process #quartets #chunks #puzzlings #chunks \n"); fprintf(ofp, "-----------------------------------------------\n"); for (n=0; n wallmax) wallmax=fullwalltimes[n]; cpusum += fullcputimes[n]; } /* for */ fprintf(ofp, "----------------------------------------------------------------------------\n"); fprintf(ofp, "Sum/Max: %11.1f %9.1f %9.1f | %11.1f %9.1f %9.1f \n", cpusum, cpusum/60, cpusum/3600, wallmax, wallmax/60, wallmax/3600); #else /* TIMEDEBUG */ fprintf(ofp, "\n\nBelow the distribution of computing times (wallclock) per host is shown.\n"); fprintf(ofp, "The times are shown in seconds, minutes, and hours. At the bottom of the table the\n"); fprintf(ofp, "the maximum wallclock times is shown.\n\n"); fprintf(ofp, "process wallclock[s] [min] [hours] \n"); fprintf(ofp, "----------------------------------------------------------------------------\n"); for (n=0; n wallmax) wallmax=fullwalltimes[n]; cpusum += fullcputimes[n]; } /* for */ fprintf(ofp, "----------------------------------------------------------------------------\n"); fprintf(ofp, "Sum/Max: %11.1f %9.1f %9.1f \n", wallmax, wallmax/60, wallmax/3600); #endif /* TIMEDEBUG */ fullcpu = cpusum; fulltime = wallmax; } /* writetimesstat */ #endif /* write current user tree to file */ void writecutree(FILE *ofp, int num) { int df; double pval, delta; if (typ_optn == TREERECON_OPTN) { /***************************************************************************/ /* MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE #xxx (NO CLOCK) */ /***************************************************************************/ if (puzzlemode == USERTREE) { fprintf(ofp, "\n\nMAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER"); fprintf(ofp, " DEFINED TREE # %d (NO CLOCK)\n\nBranch lengths are computed using", num); fprintf(ofp, " the selected model of\nsubstitution and rate heterogeneity.\n\n\n"); clockmode = 0; /* nonclocklike branch lengths */ prtopology(ofp); fprintf(ofp, "\n"); resulttree(ofp, usebranch_optn); fprintf(ofp, "\n\nUnrooted user defined tree with maximum likelihood branch lengths"); fprintf(ofp, "\n(in CLUSTAL W notation):\n\n"); fputphylogeny(ofp); fflush(ofp); /*****************************************************************************/ /* MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE #xxx (WITH CLOCK) */ /*****************************************************************************/ if (compclock) { fprintf(ofp, "\n\nMAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER"); fprintf(ofp, " DEFINED TREE # %d (WITH CLOCK)\n\nBranch lengths are computed using", num); fprintf(ofp, " the selected model of\nsubstitution and rate heterogeneity.\n"); fprintf(ofp, "\nRoot located at branch: %d ", locroot+1); if (locroot 1) fprintf(ofp, "- WARNING: %d best locations found! -", numbestroot); fprintf(ofp, "\n\n"); fprintf(ofp, "If the automatic search misplaces the root please rerun the analysis\n"); fprintf(ofp, "and select location of root manually!"); fprintf(ofp, "\n\n\n"); } if (rootsearch == ROOT_DISPLAYED) fprintf(ofp, "(displayed outgroup)\n\n\n"); clockmode = 1; /* clocklike branch lengths */ prtopology(ofp); fprintf(ofp, "\n"); resulttree(ofp, usebranch_optn); fprintf(ofp, "\n"); resultheights(ofp); fprintf(ofp, "\n\nRooted user defined tree with clocklike "); fprintf(ofp, "maximum likelihood branch lengths\n"); fprintf(ofp, "(in CLUSTAL W notation):\n\n"); fputrooted(ofp, locroot); fflush(ofp); } /*****************************************************************************/ /* MOLECULAR CLOCK LIKELIHOOD RATIO TEST FOR USER TREE #xxx */ /*****************************************************************************/ if (compclock) { fprintf(ofp, "\n\nMOLECULAR CLOCK LIKELIHOOD RATIO TEST FOR USER TREE # %d\n\n", num); fprintf(ofp, "log L without clock: %.2f (independent branch parameters: %d)\n", Ctree->lklhd, Numspc + Numibrnch); fprintf(ofp, "log L with clock: %.2f (independent branch parameters: %d)\n\n", Ctree->lklhdc, Numhts + 1); delta = fabs(2.0*((Ctree->lklhd) - (Ctree->lklhdc))); fprintf(ofp, "Likelihood ratio test statistic delta: %.2f\n", delta); df = Numspc + Numibrnch - Numhts - 1; fprintf(ofp, "Degrees of freedom of chi-square distribution: %d\n", df); pval = IncompleteGammaQ (df*0.5, delta*0.5); fprintf(ofp, "Critical significance level: %.2f%%\n\n", pval*100.0); if (pval >= 0.05) { fprintf(ofp, "The simpler (clocklike) tree can not be rejected on a significance\n"); fprintf(ofp, "level of 5%%. The log-likelihood of the more complex (no clock) tree\n"); fprintf(ofp, "is not significantly increased.\n"); } else { fprintf(ofp, "The simpler (clocklike) tree is rejected on a significance level\n"); fprintf(ofp, "of 5%%. The log-likelihood of the more complex (no clock) tree is\n"); fprintf(ofp, "significantly increased.\n"); } fprintf(ofp, "\nPlease take care that the correct root is used!\n"); } } } } /* writecutree */ /******************************************************************************/ /* timer routines */ /******************************************************************************/ void resetqblocktime(timearray_t *ta) { ta->quartcpu += ta->quartblockcpu; ta->quartblockcpu = 0.0; ta->quarttime += ta->quartblocktime; ta->quartblocktime = 0.0; } /* resetqblocktime */ void resetpblocktime(timearray_t *ta) { ta->puzzcpu += ta->puzzblockcpu; ta->puzzblockcpu = 0.0; ta->puzztime += ta->puzzblocktime; ta->puzzblocktime = 0.0; } /* resetpblocktime */ #ifdef TIMEDEBUG void printtimearr(timearray_t *ta) { # if ! PARALLEL int PP_Myid; PP_Myid = -1; # endif printf("(%2d) MMCPU: %11ld / %11ld \n", PP_Myid, ta->maxcpu, ta->mincpu); printf("(%2d) CTick: %11.6f [tks] / %11.6f [s] \n", PP_Myid, ta->mincputick, ta->mincputicktime); printf("(%2d) MMTIM: %11ld / %11ld \n", PP_Myid, ta->maxtime, ta->mintime); printf("(%2d) Mxblk: %11.6e / %11.6e \n", PP_Myid, ta->maxcpublock, ta->maxtimeblock); printf("(%2d) Mnblk: %11.6e / %11.6e \n", PP_Myid, ta->mincpublock, ta->mintimeblock); printf("(%2d) Gnrl: %11.6e / %11.6e \n", PP_Myid, ta->generalcpu, ta->generaltime); printf("(%2d) Optn: %11.6e / %11.6e \n", PP_Myid, ta->optionscpu, ta->optionstime); printf("(%2d) Estm: %11.6e / %11.6e \n", PP_Myid, ta->paramestcpu, ta->paramesttime); printf("(%2d) Qurt: %11.6e / %11.6e \n", PP_Myid, ta->quartcpu, ta->quarttime); printf("(%2d) QBlk: %11.6e / %11.6e \n", PP_Myid, ta->quartblockcpu, ta->quartblocktime); printf("(%2d) QMax: %11.6e / %11.6e \n", PP_Myid, ta->quartmaxcpu, ta->quartmaxtime); printf("(%2d) QMin: %11.6e / %11.6e \n", PP_Myid, ta->quartmincpu, ta->quartmintime); printf("(%2d) Puzz: %11.6e / %11.6e \n", PP_Myid, ta->puzzcpu, ta->puzztime); printf("(%2d) PBlk: %11.6e / %11.6e \n", PP_Myid, ta->puzzblockcpu, ta->puzzblocktime); printf("(%2d) PMax: %11.6e / %11.6e \n", PP_Myid, ta->puzzmaxcpu, ta->puzzmaxtime); printf("(%2d) PMin: %11.6e / %11.6e \n", PP_Myid, ta->puzzmincpu, ta->puzzmintime); printf("(%2d) Tree: %11.6e / %11.6e \n", PP_Myid, ta->treecpu, ta->treetime); printf("(%2d) TBlk: %11.6e / %11.6e \n", PP_Myid, ta->treeblockcpu, ta->treeblocktime); printf("(%2d) TMax: %11.6e / %11.6e \n", PP_Myid, ta->treemaxcpu, ta->treemaxtime); printf("(%2d) TMin: %11.6e / %11.6e \n", PP_Myid, ta->treemincpu, ta->treemintime); printf("(%2d) C/T : %11.6e / %11.6e \n", PP_Myid, (ta->generalcpu + ta->optionscpu + ta->paramestcpu + ta->quartblockcpu + ta->puzzblockcpu + ta->treeblockcpu), (ta->generaltime + ta->optionstime + ta->paramesttime + ta->quartblocktime + ta->puzzblocktime + ta->treeblocktime)); printf("(%2d) CPU: %11.6e / Time: %11.6e \n", PP_Myid, ta->cpu, ta->time); printf("(%2d) aCPU: %11.6e / aTime: %11.6e \n", PP_Myid, ta->fullcpu, ta->fulltime); } /* printtimearr */ #endif /* TIMEDEBUG */ char *jtype [7]; void inittimearr(timearray_t *ta) { clock_t c0, c1, c2; jtype[OVERALL] = "OVERALL"; jtype[GENERAL] = "GENERAL"; jtype[OPTIONS] = "OPTIONS"; jtype[PARAMEST] = "PARAMeter ESTimation"; jtype[QUARTETS] = "QUARTETS"; jtype[PUZZLING] = "PUZZLING steps"; jtype[TREEEVAL] = "TREE EVALuation"; ta->currentjob = GENERAL; c1 = clock(); c2 = clock(); while (c1 == c2) c2 = clock(); ta->mincputick = (double)(c2 - c1); ta->mincputicktime = ((double)(c2 - c1))/CLOCKS_PER_SEC; ta->tempcpu = clock(); ta->tempcpustart = ta->tempcpu; ta->tempfullcpu = ta->tempcpu; time(&(ta->temptime)); ta->temptimestart = ta->temptime; ta->tempfulltime = ta->temptime; c0=0; c1=0; c2=(clock_t)((2 * c1) + 1);; while (c1 < c2) { c0 = c1; c1 = c2; c2 = (clock_t)((2 * c1) + 1); } if (c1 == c2) ta->maxcpu=c0; if (c1 > c2) ta->maxcpu=c1; c0=0; c1=0; c2=(clock_t)((2 * c1) - 1); while (c1 > c2) { c0 = c1; c1 = c2; c2 = (clock_t)((2 * c1) - 1); } if (c1 == c2) ta->mincpu=c0; if (c1 < c2) ta->mincpu=c1; ta->maxtime = 0; ta->mintime = 0; ta->maxcpublock = 0; ta->mincpublock = DBL_MAX; ta->maxtimeblock = 0; ta->mintimeblock = DBL_MAX; ta->cpu = 0.0; ta->time = 0.0; ta->fullcpu = 0.0; ta->fulltime = 0.0; ta->generalcpu = 0.0; ta->optionscpu = 0.0; ta->paramestcpu = 0.0; ta->quartcpu = 0.0; ta->quartblockcpu = 0.0; ta->quartmaxcpu = 0.0; ta->quartmincpu = ((double) ta->maxcpu)/CLOCKS_PER_SEC; ta->puzzcpu = 0.0; ta->puzzblockcpu = 0.0; ta->puzzmaxcpu = 0.0; ta->puzzmincpu = ((double) ta->maxcpu)/CLOCKS_PER_SEC; ta->treecpu = 0.0; ta->treeblockcpu = 0.0; ta->treemaxcpu = 0.0; ta->treemincpu = ((double) ta->maxcpu)/CLOCKS_PER_SEC; ta->generaltime = 0.0; ta->optionstime = 0.0; ta->paramesttime = 0.0; ta->quarttime = 0.0; ta->quartblocktime = 0.0; ta->quartmaxtime = 0.0; ta->quartmintime = DBL_MAX; ta->puzztime = 0.0; ta->puzzblocktime = 0.0; ta->puzzmaxtime = 0.0; ta->puzzmintime = DBL_MAX; ta->treetime = 0.0; ta->treeblocktime = 0.0; ta->treemaxtime = 0.0; ta->treemintime = DBL_MAX; } /* inittimearr */ /***************/ void addup(int jobtype, clock_t c1, clock_t c2, time_t t1, time_t t2, timearray_t *ta) { double c, t; if (t2 != t1) t = difftime(t2, t1); else t = 0.0; if (c2 < c1) c = ((double)(c2 - ta->mincpu))/CLOCKS_PER_SEC + ((double)(ta->maxcpu - c1))/CLOCKS_PER_SEC; else c = ((double)(c2 - c1))/CLOCKS_PER_SEC; if (jobtype != OVERALL) { if (ta->mincpublock > c) ta->mincpublock = c; if (ta->maxcpublock < c) ta->maxcpublock = c; if (ta->mintimeblock > t) ta->mintimeblock = t; if (ta->maxtimeblock < t) ta->maxtimeblock = t; switch (jobtype) { case GENERAL: ta->generalcpu += c; ta->generaltime += t; break; case OPTIONS: ta->optionscpu += c; ta->optionstime += t; break; case PARAMEST: ta->paramestcpu += c; ta->paramesttime += t; break; case QUARTETS: ta->quartblockcpu += c; ta->quartblocktime += t; if (ta->quartmincpu > c) ta->quartmincpu = c; if (ta->quartmaxcpu < c) ta->quartmaxcpu = c; if (ta->quartmintime > t) ta->quartmintime = t; if (ta->quartmaxtime < t) ta->quartmaxtime = t; break; case PUZZLING: ta->puzzblockcpu += c; ta->puzzblocktime += t; if (ta->puzzmincpu > c) ta->puzzmincpu = c; if (ta->puzzmaxcpu < c) ta->puzzmaxcpu = c; if (ta->puzzmintime > t) ta->puzzmintime = t; if (ta->puzzmaxtime < t) ta->puzzmaxtime = t; break; case TREEEVAL: ta->treeblockcpu += c; ta->treeblocktime += t; if (ta->treemincpu > c) ta->treemincpu = c; if (ta->treemaxcpu < c) ta->treemaxcpu = c; if (ta->treemintime > t) ta->treemintime = t; if (ta->treemaxtime < t) ta->treemaxtime = t; break; } ta->cpu += c; ta->time += t; } else { ta->fullcpu += c; ta->fulltime += t; } # ifdef TIMEDEBUG { # if ! PARALLEL int PP_Myid = -1; # endif /* !PARALLEL */ printf("(%2d) CPU: +%10.6f / Time: +%10.6f (%s)\n", PP_Myid, c, t, jtype[jobtype]); printf("(%2d) CPU: %11.6f / Time: %11.6f (%s)\n", PP_Myid, ta->cpu, ta->time, jtype[jobtype]); printf("(%2d) CPU: %11.6f / Time: %11.6f (%s)\n", PP_Myid, ta->fullcpu, ta->fulltime, jtype[jobtype]); } # endif /* TIMEDEBUG */ } /* addup */ /***************/ void addtimes(int jobtype, timearray_t *ta) { clock_t tempc; time_t tempt; time(&tempt); tempc = clock(); if ((tempc < ta->tempfullcpu) || (jobtype == OVERALL)) { /* CPU counter overflow for overall time */ addup(OVERALL, ta->tempfullcpu, tempc, ta->tempfulltime, tempt, ta); ta->tempfullcpu = tempc; ta->tempfulltime = tempt; if (jobtype == OVERALL) { addup(ta->currentjob, ta->tempcpustart, tempc, ta->temptimestart, tempt, ta); ta->tempcpustart = ta->tempcpu; ta->tempcpu = tempc; ta->temptimestart = ta->temptime; ta->temptime = tempt; } } if((jobtype != ta->currentjob) && (jobtype != OVERALL)) { /* change of job type */ addup(ta->currentjob, ta->tempcpustart, ta->tempcpu, ta->temptimestart, ta->temptime, ta); ta->tempcpustart = ta->tempcpu; ta->tempcpu = tempc; ta->temptimestart = ta->temptime; ta->temptime = tempt; ta->currentjob = jobtype; } if (tempc < ta->tempcpustart) { /* CPU counter overflow */ addup(jobtype, ta->tempcpustart, tempc, ta->temptimestart, tempt, ta); ta->tempcpustart = ta->tempcpu; ta->tempcpu = tempc; ta->temptimestart = ta->temptime; ta->temptime = tempt; } } /* addtimes */ /******************************************************************************/ /* moved to mlparam.c */ /******************************************************************************/ #if 0 /* estimate parameters of substitution process and rate heterogeneity - no tree n-taxon tree is not needed because of quartet method or NJ tree topology */ void estimateparametersnotree() /* moved to mlparam.c */ /* estimate parameters of substitution process and rate heterogeneity - tree same as above but here the n-taxon tree is already in memory */ void estimateparameterstree() /* moved to mlparam.c */ #endif /******************************************************************************/ /* exported from main */ /******************************************************************************/ void compute_quartlklhds(int a, int b, int c, int d, double *d1, double *d2, double *d3, int approx) { if (approx == APPROX) { *d1 = quartet_alklhd(a,b, c,d); /* (a,b)-(c,d) */ *d2 = quartet_alklhd(a,c, b,d); /* (a,c)-(b,d) */ *d3 = quartet_alklhd(a,d, b,c); /* (a,d)-(b,c) */ } else /* approx == EXACT */ { *d1 = quartet_lklhd(a,b, c,d); /* (a,b)-(c,d) */ *d2 = quartet_lklhd(a,c, b,d); /* (a,c)-(b,d) */ *d3 = quartet_lklhd(a,d, b,c); /* (a,d)-(b,c) */ } } /* compute_quartlklhds */ /***************************************************************/ /* Reconstruct a tree with QP */ /* (parameter estimation already done) */ void recon_tree() { int i; unsigned char tmpweight; /***********************************/ /*** allocation + initialization ***/ /***********************************/ /* allocate and initialize qinfomatr */ qinfomatr = new_ulimatrix(9,Maxspc); for (i = 0; i < Maxspc; i++) { qinfomatr[0][i] = 0; /* missing quartets */ qinfomatr[1][i] = 0; /* fully resolved quartet 1 for taxon i */ qinfomatr[2][i] = 0; /* fully resolved quartet 2 for taxon i */ qinfomatr[3][i] = 0; /* fully resolved quartet 3 for taxon i */ qinfomatr[4][i] = 0; /* partly resolved quartet 1 for taxon i */ qinfomatr[5][i] = 0; /* partly resolved quartet 2 for taxon i */ qinfomatr[6][i] = 0; /* partly resolved quartet 3 for taxon i */ qinfomatr[7][i] = 0; /* unresolved quartet for taxon i */ qinfomatr[8][i] = 0; /* sum of quartets for taxon i */ } /* allocate memory for taxon list of bad quartets */ badtaxon = new_ulivector(Maxspc); for (i = 0; i < Maxspc; i++) badtaxon[i] = 0; /* allocate memory for quartets */ quartetinfo = callocquartets(Maxspc); /* prepare for consensus tree analysis */ initconsensus(); time(&MLstepStarttime); # ifdef DEBUG_PRINTTIMES fprintftimespan(stdout, PEstStoptime, MLstepStarttime, Starttime, "PEst -> MLstep"); # endif /* DEBUG_PRINTTIMES */ /***************/ /*** ML step ***/ /***************/ if (!(readquart_optn) || (readquart_optn && savequart_optn)) { /* compute quartets */ fprintf(STDOUT, "Computing quartet maximum likelihood trees\n"); fflush(STDOUT); computeallquartets(); } time(&MLstepStoptime); # ifdef DEBUG_PRINTTIMES fprintftimespan(stdout, MLstepStarttime, MLstepStoptime, Starttime, "MLstep"); # endif /* DEBUG_PRINTTIMES */ /** output/input if necessary **/ if (savequart_optn) writeallquarts(Maxspc, ALLQUART, quartetinfo); if (readquart_optn) { readallquarts (Maxspc, ALLQUART, quartetinfo); if (show_optn) { /* list all unresolved quartets */ openfiletowrite(&unresfp, UNRESOLVED, "unresolved quartet trees"); fprintf(unresfp, "List of all completely unresolved quartets:\n\n"); } if (readsubset_optn) { /* missing data -> read subsets */ FILE *ssfp; openfiletoread(&ssfp, SUBSET, "taxon subsets"); fprintf(STDOUT, "Reading taxon subsets: %s\n", SUBSET); readsubsetfile(ssfp, Maxspc, Namestr, &Maxsubset, &ss_setovlgraph, &ss_setoverlaps, &ss_setovllist, &ss_setovllistsize, &ss_matrix, &ss_list, &ss_listsize); #if 0 fprintf(stderr,"Maxspc=%d Maxsubset=%d\n", Maxspc, Maxsubset); fprintfss(stdout, Maxspc, Maxsubset, ss_setovlgraph, ss_setoverlaps, ss_setovllist, ss_setovllistsize, ss_matrix, ss_list, ss_listsize); #endif checkss(stdout, Maxspc, Maxsubset, ss_setovlgraph, ss_setoverlaps, ss_setovllist, ss_setovllistsize, ss_matrix, ss_list, ss_listsize); } } /* readquart_optn */ # if !PARALLEL /* do it every time in case of a parallel run - less comunication */ if (readquart_optn) # endif /* PARALLEL */ { int xx1, xx2, xx3, xx4, count; /* initialize qinfomatr */ for (i = 0; i < Maxspc; i++) { qinfomatr[0][i] = 0; /* missing quartets */ qinfomatr[1][i] = 0; /* fully resolved quartet 1 for taxon i */ qinfomatr[2][i] = 0; /* fully resolved quartet 2 for taxon i */ qinfomatr[3][i] = 0; /* fully resolved quartet 3 for taxon i */ qinfomatr[4][i] = 0; /* partly resolved quartet 1 for taxon i */ qinfomatr[5][i] = 0; /* partly resolved quartet 2 for taxon i */ qinfomatr[6][i] = 0; /* partly resolved quartet 3 for taxon i */ qinfomatr[7][i] = 0; /* unresolved quartet for taxon i */ qinfomatr[8][i] = 0; /* sum of quartets for taxon i */ } /* initialize bad quartet memory */ for (count = 0; count < Maxspc; count++) badtaxon[count] = 0; badqs = 0; fullresqs = 0; partresqs = 0; unresqs = 0; missingqs = 0; for (xx4 = 3; xx4 < Maxspc; xx4++) for (xx3 = 2; xx3 < xx4; xx3++) for (xx2 = 1; xx2 < xx3; xx2++) for (xx1 = 0; xx1 < xx2; xx1++) { tmpweight = readquartet(xx1, xx2, xx3, xx4); /* compute sums of topologies per taxon, step by step */ ++(qinfomatr[8][xx1]); ++(qinfomatr[8][xx2]); ++(qinfomatr[8][xx3]); ++(qinfomatr[8][xx4]); ++(qinfomatr[tmpweight][xx1]); ++(qinfomatr[tmpweight][xx2]); ++(qinfomatr[tmpweight][xx3]); ++(qinfomatr[tmpweight][xx4]); if ((tmpweight <= 2) || (tmpweight == 4)) { fullresqs++; } else { if (tmpweight == 7) { unresqs++; } else { if (tmpweight == 0) { missingqs++; } else { partresqs++; } } } if (tmpweight == 7) { /* to be deleted */ badqs++; badtaxon[xx1]++; badtaxon[xx2]++; badtaxon[xx3]++; badtaxon[xx4]++; if (show_optn) { fputid10(unresfp, xx1); fprintf(unresfp, " "); fputid10(unresfp, xx2); fprintf(unresfp, " "); fputid10(unresfp, xx3); fprintf(unresfp, " "); fputid (unresfp, xx4); fprintf(unresfp, "\n"); } /* if show_optn */ } /* if 7 */ /* to be deleted */ } /* end for xx4; for xx3; for xx2; for xx1 */ if (show_optn) /* list all unresolved quartets */ fclose(unresfp); } /* readquart_optn */ # if PARALLEL PP_SendAllQuarts(numquarts(Maxspc), quartetinfo); # endif /* PARALLEL */ /*********************/ /*** puzzling step ***/ /*********************/ fprintf(STDOUT, "Computing quartet puzzling trees\n"); fflush(STDOUT); /* start timer - percentage of completed trees */ time(&time0); time1 = time0; mflag = 0; time(&PStepStarttime); # ifdef DEBUG_PRINTTIMES fprintftimespan(stdout, MLstepStoptime, PStepStarttime, Starttime, "MLstep -> Pstep"); # endif /* DEBUG_PRINTTIMES */ /* open file for chronological list of puzzling step trees */ if((listqptrees == PSTOUT_LIST) || (listqptrees == PSTOUT_LISTORDER)) openfiletowrite(&qptlist, OUTPTLIST, "puzzling step trees (chonological)"); # if PARALLEL PP_SendDoPermutBlock(Numtrial); # else /* ! PARALLEL */ addtimes(GENERAL, &tarr); /* loop exported to allpstep */ allpstep(Numtrial, quartetinfo, Maxspc, fixedorder_optn); # endif /* else ! PARALLEL */ time(&PStepStoptime); # ifdef DEBUG_PRINTTIMES fprintftimespan(stdout, PStepStarttime, PStepStoptime, Starttime, "Pstep"); # endif /* DEBUG_PRINTTIMES */ /* close file for list of puzzling step trees */ if((listqptrees == PSTOUT_LIST) || (listqptrees == PSTOUT_LISTORDER)) closefile(qptlist); if (mflag == 1) fprintf(STDOUT, "\n"); /* garbage collection */ free(splitcomptemp); # if ! PARALLEL free_cmatrix(biparts); # endif /* ! PARALLEL */ /**********************/ /*** consensus step ***/ /**********************/ /* compute majority rule consensus tree */ makeconsensus(Numtrial, qsupport_optn); /* write consensus tree to tmp file */ #if 0 if (skipmlbranch_optn && (puzzlemode == QUARTPUZ)) #endif if (!dotreelh_optn && (puzzlemode == QUARTPUZ)) { openfiletowrite(&tmpfp, TREEFILE, "output tree(s)"); writeconsensustree(tmpfp, FALSE, qsupportarr); closefile(tmpfp); } else { tmpfp = tmpfile(); writeconsensustree(tmpfp, FALSE, qsupportarr); } } /* recon_tree */ /***************************************************************/ void map_lklhd() { int i, a, a1, a2, b, b1, b2, c, c1, c2, d; uli nq; double logs[3], d1, d2, d3, temp; ivector qts, mlorder, gettwo; /* reset variables */ ar1 = ar2 = ar3 = 0; reg1 = reg2 = reg3 = reg4 = reg5 = reg6 = reg7 = 0; reg1l = reg1r = reg2u = reg2d = reg3u = reg3d = reg4u = reg4d = reg5l = reg5r = reg6u = reg6d = 0; /* place for random quartet */ qts = new_ivector(4); /* initialize output file */ openfiletowrite(&trifp, TRIANGLE, "Postscript output"); initps(trifp); fprintf(STDOUT, "Performing likelihood mapping analysis\n"); fflush(STDOUT); nq = 0; mflag = 0; addtimes(GENERAL, &tarr); if (lmqts == 0) { /* all possible quartets */ if (numclust == 4) { /* four-cluster analysis */ for (a = 0; a < clustA; a++) for (b = 0; b < clustB; b++) for (c = 0; c < clustC; c++) for (d = 0; d < clustD; d++) { nq++; /* maximum likelihood values */ /* approximate ML is sufficient */ compute_quartlklhds(clusterA[a],clusterB[b],clusterC[c],clusterD[d],&d1,&d2,&d3, APPROX); /* draw point for LM analysis */ makelmpoint(trifp, d1, d2, d3); addtimes(QUARTETS, &tarr); } } if (numclust == 3) { /* three-cluster analysis */ gettwo = new_ivector(2); for (a = 0; a < clustA; a++) for (b = 0; b < clustB; b++) for (c1 = 0; c1 < clustC-1; c1++) for (c2 = c1+1; c2 < clustC; c2++) { nq++; /* maximum likelihood values */ /* approximate ML is sufficient */ compute_quartlklhds(clusterA[a],clusterB[b],clusterC[c1],clusterC[c2],&d1,&d2,&d3, APPROX); /* randomize order of d2 and d3 */ if (randominteger(2) == 1) { temp = d3; d3 = d2; d2 = temp; } /* draw point for LM analysis */ makelmpoint(trifp, d1, d2, d3); addtimes(QUARTETS, &tarr); } free_ivector(gettwo); } if (numclust == 2) { /* two-cluster analysis */ gettwo = new_ivector(2); for (a1 = 0; a1 < clustA-1; a1++) for (a2 = a1+1; a2 < clustA; a2++) for (b1 = 0; b1 < clustB-1; b1++) for (b2 = b1+1; b2 < clustB; b2++) { nq++; /* maximum likelihood values */ /* approximate ML is sufficient */ compute_quartlklhds(clusterA[a1],clusterA[a2],clusterB[b1],clusterB[b2],&d1,&d2,&d3, APPROX); /* randomize order of d2 and d3 */ if (randominteger(2) == 1) { temp = d3; d3 = d2; d2 = temp; } /* draw point for LM analysis */ makelmpoint(trifp, d1, d2, d3); addtimes(QUARTETS, &tarr); } free_ivector(gettwo); } if (numclust == 1) { /* normal likelihood mapping (one cluster) */ mlorder = new_ivector(3); for (i = 3; i < Maxspc; i++) for (c = 2; c < i; c++) for (b = 1; b < c; b++) for (a = 0; a < b; a++) { nq++; /* maximum likelihood values */ /* approximate ML is sufficient */ compute_quartlklhds(a,b,c,i,&logs[0],&logs[1],&logs[2], APPROX); /* randomize order */ chooser(3,3,mlorder); d1 = logs[mlorder[0]]; d2 = logs[mlorder[1]]; d3 = logs[mlorder[2]]; /* draw point for LM analysis */ makelmpoint(trifp, d1, d2, d3); addtimes(QUARTETS, &tarr); } free_ivector(mlorder); } } else { /* randomly selected quartets */ if (numclust == 4) { /* four-cluster analysis */ for (lmqts = 0; lmqts < Numquartets; lmqts++) { nq++; /* choose random quartet */ qts[0] = clusterA[ randominteger(clustA) ]; qts[1] = clusterB[ randominteger(clustB) ]; qts[2] = clusterC[ randominteger(clustC) ]; qts[3] = clusterD[ randominteger(clustD) ]; /* maximum likelihood values */ /* approximate ML is sufficient */ compute_quartlklhds(qts[0],qts[1],qts[2],qts[3],&d1,&d2,&d3, APPROX); /* draw point for LM analysis */ makelmpoint(trifp, d1, d2, d3); addtimes(QUARTETS, &tarr); } } if (numclust == 3) { /* three-cluster analysis */ gettwo = new_ivector(2); for (lmqts = 0; lmqts < Numquartets; lmqts++) { nq++; /* choose random quartet */ qts[0] = clusterA[ randominteger(clustA) ]; qts[1] = clusterB[ randominteger(clustB) ]; chooser(clustC, 2, gettwo); qts[2] = clusterC[gettwo[0]]; qts[3] = clusterC[gettwo[1]]; /* maximum likelihood values */ /* approximate ML is sufficient */ compute_quartlklhds(qts[0],qts[1],qts[2],qts[3],&d1,&d2,&d3, APPROX); /* order of d2 and d3 is already randomized! */ /* draw point for LM analysis */ makelmpoint(trifp, d1, d2, d3); addtimes(QUARTETS, &tarr); } free_ivector(gettwo); } if (numclust == 2) { /* two-cluster analysis */ gettwo = new_ivector(2); for (lmqts = 0; lmqts < Numquartets; lmqts++) { nq++; /* choose random quartet */ chooser(clustA, 2, gettwo); qts[0] = clusterA[gettwo[0]]; qts[1] = clusterA[gettwo[1]]; chooser(clustB, 2, gettwo); qts[2] = clusterB[gettwo[0]]; qts[3] = clusterB[gettwo[1]]; /* maximum likelihood values */ /* approximate ML is sufficient */ compute_quartlklhds(qts[0],qts[1],qts[2],qts[3],&d1,&d2,&d3, APPROX); /* order of d2 and d3 is already randomized! */ /* draw point for LM analysis */ makelmpoint(trifp, d1, d2, d3); addtimes(QUARTETS, &tarr); } free_ivector(gettwo); } if (numclust == 1) { /* normal likelihood mapping (one cluster) */ for (lmqts = 0; lmqts < Numquartets; lmqts++) { nq++; /* choose random quartet */ chooser(Maxspc, 4, qts); /* maximum likelihood values */ /* approximate ML is sufficient */ compute_quartlklhds(qts[0],qts[1],qts[2],qts[3],&d1,&d2,&d3, APPROX); /* order of d1, d2, and d3 is already randomized! */ /* draw point for LM analysis */ makelmpoint(trifp, d1, d2, d3); addtimes(QUARTETS, &tarr); } } } finishps(trifp); closefile(trifp); free_ivector(qts); } /* map_lklhd */ /***************************************************************/ void setdefaults() { strcpy(INFILE, INFILEDEFAULT); strcpy(OUTFILE, OUTFILEDEFAULT); strcpy(TREEFILE, TREEFILEDEFAULT); strcpy(INTREE, INTREEDEFAULT); strcpy(DISTANCES, DISTANCESDEFAULT); strcpy(TRIANGLE, TRIANGLEDEFAULT); strcpy(UNRESOLVED, UNRESOLVEDDEFAULT); strcpy(ALLQUART, ALLQUARTDEFAULT); strcpy(ALLQUARTLH, ALLQUARTLHDEFAULT); strcpy(SITELH, SITELHDEFAULT); strcpy(SITELHB, SITELHBDEFAULT); strcpy(SITERATE, SITERATEDEFAULT); strcpy(SITERATEB, SITERATEBDEFAULT); strcpy(OUTPARAM, OUTPARAMDEFAULT); strcpy(SUBSET, SUBSETDEFAULT); strcpy(OUTPTLIST, OUTPTLISTDEFAULT); strcpy(OUTPTORDER, OUTPTORDERDEFAULT); setprefix_optn = SETPREFIX_NONE; /* 0: not set */ /* 1: INFILE */ /* 2: INTREE */ /* 3: reset by openfileto... */ /* 4: -prefix= */ usebestq_optn = FALSE; usebranch_optn = FALSE; printrmatr_optn = FALSE; savequartlh_optn = FALSE; savequart_optn = FALSE; readquart_optn = FALSE; fixedorder_optn = FALSE; #if 0 skipmlbranch_optn = FALSE; #endif conssub50_optn = FALSE; qsupport_optn = FALSE; dotreetest_optn = TRUE; dotreelh_optn = TRUE; savesitelhb_optn = FALSE; savesitelh_optn = FALSE; savesiterateb_optn = FALSE; savesiterate_optn = FALSE; consensus_optn = FALSE; readsubset_optn = FALSE; #if 0 saveparam_optn = FALSE; #endif randseed = -1; /* to set random random seed */ } /* setdefaults */ /***************************************************************/ void printversion(char *fname) { # if ! PARALLEL fprintf(stderr, "puzzle (%s) %s\n", PACKAGE, VERSION); #else fprintf(stderr, "ppuzzle (%s) %s\n", PACKAGE, VERSION); PP_SendDone(); MPI_Finalize(); # endif exit (0); } /* printversion */ /***************************************************************/ void printusage(char *fname) { /* |<--- 80 characters --->| */ fprintf(stderr, "\n\nUsage: %s [-h] [options] [ Infilename [ UserTreeFilename ] ]\n\n", fname); fprintf(stderr, " -h - print usage\n"); fprintf(stderr, " -prefix=XXX - use 'XXX' as filename prefix instead of 'Infilename'\n"); fprintf(stderr, " of 'Infilename' or 'UserTreeFilename'\n"); fprintf(stderr, " -consmrel - perform consensus step below 50%% to first incongruence,\n"); fprintf(stderr, " that is a 'relative mayority consensus' is built.\n"); fprintf(stderr, " -randseed<#> \n"); fprintf(stderr, " -randseed=<#> - use <#> as random number seed, for debug purposes only\n"); fprintf(stderr, " Infilename - Filename of multiple sequence alignment in PHYLIP format\n"); fprintf(stderr, " UserTreeFilename - Filename of the treefile in PHYLIP format\n"); # if PARALLEL PP_SendDone(); MPI_Finalize(); # endif exit (1); } /* printusage */ /***************************************************************/ void printusagehhh(char *fname) { fprintf(stderr, "\n\nUsage: %s [options] [ Infilename [ UserTreeFilename ] ]\n\n", fname); /* |<--- 80 characters --->| */ fprintf(stderr, " -h - print usage\n"); fprintf(stderr, " -prefix=XXX - use 'XXX' as filename prefix instead of 'Infilename'\n"); fprintf(stderr, " of 'Infilename' or 'UserTreeFilename'\n"); fprintf(stderr, " -consmrel\n"); fprintf(stderr, " -sub50 - perform consensus step below 50%% to first incongruence\n"); fprintf(stderr, " -randseed<#> \n"); fprintf(stderr, " -randseed=<#> - use <#> as random number seed, for debug purposes only\n"); fprintf(stderr, " -wqf - write quartet file to PREFIX.allquart\n"); fprintf(stderr, " -rqf - read quartet file from PREFIX.allquart\n"); fprintf(stderr, " -wqlb - write quart llhs to PREFIX.allquartlh (bin) [non-parallel]\n"); fprintf(stderr, " -wqla - write quart llhs to PREFIX.allquartlh (ASCII)[non-parallel]\n"); fprintf(stderr, " -wsl - write site llhs to PREFIX.sitelh (PHILIP-like)\n"); fprintf(stderr, " -wsr - write site rates to PREFIX.siterate (PHYLIP-like)\n"); fprintf(stderr, " -bestq - use best quart, no Bayesian weights\n"); fprintf(stderr, " -printrmat - print rate matrix to screen\n"); fprintf(stderr, " -consensus - construct a consensus tree from user trees [non-parallel]\n"); fprintf(stderr, " -usebranch - use branch length from usertree file\n"); fprintf(stderr, " -achim - reads quartet set and sets puzzling step orders to 1,2,...n\n"); fprintf(stderr, " -rssm - read subset matrix from PREFIX.subsetmatr for missing data\n"); fprintf(stderr, " -notreetest - skip test for usertree topologies (KH, SH, ELW)\n"); fprintf(stderr, " -notreelh - skip likelihood/branch length (QP or consensus)\n"); fprintf(stderr, " Infilename - Filename of multiple sequence alignment in PHYLIP format\n"); fprintf(stderr, " UserTreeFilename - Filename of the treefile in PHYLIP format\n"); # ifdef USE_ADJUSTABLE_EPS fprintf(stderr, " -epsrate=# - stop threshold for rate heterogeneity estimation (%.2e)\n", EPSILON_RATEPARAM_DEFAULT); fprintf(stderr, " -epssubst=# - stop threshold for subst. parameter estimation (%.2e)\n", EPSILON_SUBSTPARAM_DEFAULT); fprintf(stderr, " -epsbranch=# - stop threshold for branch length estimation (%.2e)\n", EPSILON_BRANCH_DEFAULT); fprintf(stderr, " -epsheight=# - stop threshold for tree height estimation (%.2e)\n", EPSILON_HEIGHTS_DEFAULT); # endif fprintf(stderr, "\n"); #ifdef HHH /* |<--- 80 characters --->| */ fprintf(stderr, " not yet implemented in this version:\n"); fprintf(stderr, " -wslb - write site lhs to PREFIX.sitelhb (binary) [not yet]\n"); fprintf(stderr, " -wsrb - write site rates to PREFIX.siterateb (binary) [not yet]\n"); fprintf(stderr, " -wparam - write params to PREFIX.param [not yet]\n"); fprintf(stderr, " -qsupport - prints quartet support for incorporated splits [not yet]\n"); fprintf(stderr, " -consth=<#> - consensus threshold, e.g. 50=M_50 consensus [not yet]\n"); fprintf(stderr, " -wqnex - write quartets in nexus format [not yet]\n"); fprintf(stderr, " -wsnex - write splits in nexus format [not yet]\n"); fprintf(stderr, " -wsth=<#> - split threshold, e.g. 50 - splits of the M_50 [not yet]\n"); fprintf(stderr, " -wsnex=<#> - write splits with > <#>%% occurence - nexus format[not yet]\n"); fprintf(stderr, " -witnex - write intermediate trees in nexus format [not yet]\n"); fprintf(stderr, " -quartml - use ML values to evaluate quartets [not yet]\n"); fprintf(stderr, " -quartmlapprox - use approximate ML values to evaluate quartets [default]\n"); fprintf(stderr, " -quartnj - use NJ to evaluate quartets [not yet]\n"); fprintf(stderr, " -quartme - use ME to evaluate quartets [not yet]\n"); fprintf(stderr, " -quartpars - use parsimony to evaluate quartets [not yet]\n"); fprintf(stderr, "\n"); #endif /* HHH */ # if PARALLEL PP_SendDone(); MPI_Finalize(); # endif exit (2); } /* printusagehhh */ /***************************************************************/ /* infiletype 1=infile, 2=intree */ void setfilenames(int setprefix_optn, int infiletype, char fname[]){ # if 0 fprintf(stderr, "XXXX: %d, %d, %s\n", setprefix_optn, infiletype, fname); # endif /* set filenames, if set by -prefix=, INFILE, or INTREE */ if (setprefix_optn < SETPREFIX_PREFIX) { switch(setprefix_optn) { case SETPREFIX_INTREE: sprintf(FILEPREFIX, "%s", INTREE); break; case SETPREFIX_INFILE: sprintf(FILEPREFIX, "%s", INFILE); break; default: break; } } sprintf(OUTFILE ,"%s.%s", FILEPREFIX, OUTFILEEXT); sprintf(TREEFILE ,"%s.%s", FILEPREFIX, TREEFILEEXT); sprintf(DISTANCES ,"%s.%s", FILEPREFIX, DISTANCESEXT); sprintf(TRIANGLE ,"%s.%s", FILEPREFIX, TRIANGLEEXT); sprintf(UNRESOLVED ,"%s.%s", FILEPREFIX, UNRESOLVEDEXT); sprintf(ALLQUART ,"%s.%s", FILEPREFIX, ALLQUARTEXT); sprintf(ALLQUARTLH ,"%s.%s", FILEPREFIX, ALLQUARTLHEXT); sprintf(SITELH ,"%s.%s", FILEPREFIX, SITELHEXT); sprintf(SITELHB ,"%s.%s", FILEPREFIX, SITELHBEXT); sprintf(SITERATE ,"%s.%s", FILEPREFIX, SITERATEEXT); sprintf(SITERATEB ,"%s.%s", FILEPREFIX, SITERATEBEXT); sprintf(OUTPARAM ,"%s.%s", FILEPREFIX, OUTPARAMEXT); sprintf(SUBSET ,"%s.%s", FILEPREFIX, SUBSETEXT); sprintf(OUTPTLIST ,"%s.%s", FILEPREFIX, OUTPTLISTEXT); sprintf(OUTPTORDER ,"%s.%s", FILEPREFIX, OUTPTORDEREXT); } /* scancmdline */ /***************************************************************/ void scancmdline(int *argc, char **argv[]) { static short infileset = 0; static short intreefileset = 0; short flagused; int n; int count, dummyint; # ifdef USE_ADJUSTABLE_EPS double dummydbl; # endif for (n = 1; n < *argc; n++) { # ifdef VERBOSE1 printf("argv[%d] = %s\n", n, (*argv)[n]); # endif flagused = FALSE; /* use given prefix rather than INFILENAME for output filename */ dummyint = 0; count = sscanf((*argv)[n],"-prefix=%s%n", FILEPREFIX, &dummyint); if (dummyint>8) { printf("PREFIX set to = \"%s\"\n", FILEPREFIX); setprefix_optn = SETPREFIX_PREFIX; flagused = TRUE; } /* write quartet likelihoods (binary) - only in sequential version */ dummyint = 0; count = sscanf((*argv)[n], "-wqlb%n", &dummyint); if (dummyint == 5) { savequartlh_optn = TRUE; saveqlhbin_optn = TRUE; flagused = TRUE; } /* write quartet likelihoods (ASCII) - only in sequential version */ dummyint = 0; count = sscanf((*argv)[n], "-wqla%n", &dummyint); if (dummyint == 5) { savequartlh_optn = TRUE; saveqlhbin_optn = FALSE; flagused = TRUE; } /* write quartet topologies */ dummyint = 0; count = sscanf((*argv)[n], "-wqf%n", &dummyint); if (dummyint == 4) { savequart_optn = TRUE; flagused = TRUE; } /* read quartet topologies -> no ML step */ dummyint = 0; count = sscanf((*argv)[n],"-rqf%n", &dummyint); if (dummyint == 4) { readquart_optn = TRUE; flagused = TRUE; } /* use quartet topology with best likelihood -> no posterior probs */ dummyint = 0; count = sscanf((*argv)[n],"-bestq%n", &dummyint); if (dummyint == 6) { usebestq_optn = TRUE; flagused = TRUE; } /* print substitution matrix Q to the screen */ dummyint = 0; count = sscanf((*argv)[n],"-printrmat%n", &dummyint); if (dummyint == 10) { printrmatr_optn = TRUE; flagused = TRUE; } /* print extended help */ dummyint = 0; count = sscanf((*argv)[n],"-hhh%n", &dummyint); if (dummyint==4) { printusagehhh((*argv)[0]); flagused = TRUE; } /* resolve congruent splits < 50% (M_rel) in consensus */ dummyint = 0; count = sscanf((*argv)[n],"-sub50%n", &dummyint); if (dummyint == 6) { conssub50_optn = TRUE; flagused = TRUE; } /* resolve congruent splits < 50% (M_rel) in consensus */ dummyint = 0; count = sscanf((*argv)[n],"-consmrel%n", &dummyint); if (dummyint == 9) { conssub50_optn = TRUE; flagused = TRUE; } /* include: fixed order addition (1,2,3,...,n) */ /* no ML branch lengths for consensus */ /* read quartets from file */ dummyint = 0; count = sscanf((*argv)[n],"-achim%n", &dummyint); if (dummyint == 6) { fixedorder_optn = TRUE; #if 0 skipmlbranch_optn = TRUE; #endif dotreelh_optn = FALSE; readquart_optn = TRUE; flagused = TRUE; } # ifdef HHH /* save site likelihoods (binary) file */ dummyint = 0; count = sscanf((*argv)[n], "-wslb%n", &dummyint); if (dummyint == 5) { savesitelhb_optn = TRUE; fprintf(stderr, "cmdline option '-wslb' is not yet implemented!!!\n"); flagused = TRUE; } # endif /* HHH */ /* save site likelihoods to PHYLIP like file */ dummyint = 0; count = sscanf((*argv)[n], "-wsl%n", &dummyint); if (dummyint == 4) { savesitelh_optn = TRUE; flagused = TRUE; } # ifdef HHH /* save site rates (binary) file */ dummyint = 0; count = sscanf((*argv)[n], "-wsrb%n", &dummyint); if (dummyint == 5) { savesiterateb_optn = TRUE; fprintf(stderr, "cmdline option '-wsrb' is not yet implemented!!!\n"); flagused = TRUE; } # endif /* HHH */ /* save site rates to PHYLIP like file */ dummyint = 0; count = sscanf((*argv)[n], "-wsr%n", &dummyint); if (dummyint == 4) { savesiterate_optn = TRUE; flagused = TRUE; } /* print version */ dummyint = 0; count = sscanf((*argv)[n],"-V%n", &dummyint); if (dummyint==2) { printversion((*argv)[0]); flagused = TRUE; } /* print version */ dummyint = 0; count = sscanf((*argv)[n],"-version%n", &dummyint); if (dummyint==8) { printversion((*argv)[0]); flagused = TRUE; } /* print version */ dummyint = 0; count = sscanf((*argv)[n],"--version%n", &dummyint); if (dummyint>=4) { printversion((*argv)[0]); flagused = TRUE; } /* print help message */ dummyint = 0; count = sscanf((*argv)[n],"-h%n", &dummyint); if (dummyint==2) { printusage((*argv)[0]); flagused = TRUE; } /* set random number seed to fixed value */ count = sscanf((*argv)[n],"-randseed%d", &dummyint); if (count == 1) { randseed = dummyint; flagused = TRUE; } /* set random number seed to fixed value */ count = sscanf((*argv)[n],"-randseed=%d", &dummyint); if (count == 1) { randseed = dummyint; flagused = TRUE; } # ifdef USE_ADJUSTABLE_EPS /* set stop threshold for branch length estimation */ dummydbl=EPSILON_BRANCH_DEFAULT; count = sscanf((*argv)[n],"-epsbranch%lf", &dummydbl); if (count == 1) { EPSILON_BRANCH = dummydbl; fprintf(stderr, "branch length estimation threshold set to %e! (default=%e)\n", EPSILON_BRANCH, EPSILON_BRANCH_DEFAULT); flagused = TRUE; } /* set stop threshold for tree heights estimation */ dummydbl=EPSILON_HEIGHTS_DEFAULT; count = sscanf((*argv)[n],"-epsheight%lf", &dummydbl); if (count == 1) { EPSILON_HEIGHTS = dummydbl; fprintf(stderr, "tree heights estimation threshold set to %e! (default=%e)\n", EPSILON_HEIGHTS, EPSILON_HEIGHTS_DEFAULT); flagused = TRUE; } /* set stop threshold for rate heterogeneity estimation */ dummydbl=EPSILON_RATEPARAM_DEFAULT; count = sscanf((*argv)[n],"-epsrate%lf", &dummydbl); if (count == 1) { EPSILON_RATEPARAM = dummydbl; fprintf(stderr, "rate heterogeneity estimation threshold set to %e! (default=%.2e)\n", EPSILON_RATEPARAM, EPSILON_RATEPARAM_DEFAULT); flagused = TRUE; } /* set stop threshold for substitution model parameter estimation */ dummydbl=EPSILON_SUBSTPARAM_DEFAULT; count = sscanf((*argv)[n],"-epssubst%lf", &dummydbl); if (count == 1) { EPSILON_SUBSTPARAM = dummydbl; fprintf(stderr, "substitution model parameter estimation threshold set to %e! (default=%e)\n", EPSILON_SUBSTPARAM, EPSILON_SUBSTPARAM_DEFAULT); flagused = TRUE; } # endif /* compute consensus from usertrees (also 'k' in menu) */ dummyint = 0; count = sscanf((*argv)[n],"-consensus%n", &dummyint); if (dummyint == 10) { consensus_optn = TRUE; flagused = TRUE; } /* read branch lengths from usertree file */ dummyint = 0; count = sscanf((*argv)[n],"-usebranch%n", &dummyint); if (dummyint == 10) { usebranch_optn = TRUE; flagused = TRUE; } /* read subset matrix for missing data analysis */ dummyint = 0; count = sscanf((*argv)[n], "-rssm%n", &dummyint); if (dummyint == 5) { readsubset_optn = TRUE; readquart_optn = TRUE; flagused = TRUE; } /* write quartet support for splits */ dummyint = 0; count = sscanf((*argv)[n], "-qsupport%n", &dummyint); if (dummyint == 9) { qsupport_optn = TRUE; flagused = TRUE; } /* skip tree tests (KH,SH,ELW) */ dummyint = 0; count = sscanf((*argv)[n], "-notreetest%n", &dummyint); if (dummyint == 11) { dotreetest_optn = FALSE; flagused = TRUE; } /* skip lh/branch length computation (QP/consensus)*/ dummyint = 0; count = sscanf((*argv)[n], "-notreelh%n", &dummyint); if (dummyint == 9) { dotreelh_optn = FALSE; flagused = TRUE; } #if 0 /* use window of alignment */ /* todo (HAS) */ count = sscanf((*argv)[n],"-ws%d", &dummyint); if (count == 1) windowsize = dummyint; /* write parameter file (for resart) */ dummyint = 0; count = sscanf((*argv)[n], "-wparam%n", &dummyint); if (dummyint == 7) { saveparam_optn = TRUE; flagused = TRUE; } #endif /* get alignment filename */ if ((*argv)[n][0] != '-') { if (infileset == 0) { if (strlen((*argv)[n]) >= FILENAMELENGTH) { fprintf(STDOUT, "Unable to proceed (filename too long)\n"); fprintf(STDOUT, "You may want to recompile with FILENAMELENGTH>%d\n\n\n", FILENAMELENGTH); # if PARALLEL PP_Finalize(); # endif exit(1); } strcpy(INFILE, (*argv)[n]); infileset++; if (setprefix_optn < SETPREFIX_PREFIX) { strcpy(FILEPREFIX, INFILE); /* printf("PREFIX set to = \"%s\"\n", FILEPREFIX); */ setprefix_optn = SETPREFIX_INFILE; } fprintf(STDOUT, "Input file: %s\n", INFILE); flagused = TRUE; } else { /* get usertree filename */ if (intreefileset == 0) { if (strlen((*argv)[n]) >= FILENAMELENGTH) { fprintf(STDOUT, "Unable to proceed (filename too long)\n"); fprintf(STDOUT, "You may want to recompile with FILENAMELENGTH>%d\n\n\n", FILENAMELENGTH); # if PARALLEL PP_Finalize(); # endif exit(1); } strcpy(INTREE, (*argv)[n]); intreefileset++; if (setprefix_optn < SETPREFIX_PREFIX) { strcpy(FILEPREFIX, INTREE); /* printf("PREFIX set to = \"%s\"\n", FILEPREFIX); */ setprefix_optn = SETPREFIX_INTREE; } fprintf(STDOUT, "Usertree file: %s\n", INTREE); flagused = TRUE; } } } if (flagused == FALSE) { fprintf(stderr, "WARNING: commandline parameter %d not recognized (\"%s\")\n", n, (*argv)[n]); } flagused = FALSE; } /* setprefix_optn = SETPREFIX_INFILE; */ if (setprefix_optn > 0) { setfilenames(setprefix_optn, RESET_NONE, INFILE); } } /* scancmdline */ /***************************************************************/ void inputandinit(int *argc, char **argv[]) { int ci; int taxon; int reset; #ifdef EPE_DEBUG int i; /*epe*/ #endif /* EPE_DEBUG */ # ifndef ALPHA fprintf(STDOUT, "\n\n\nWELCOME TO TREE-PUZZLE %s!\n\n\n\n", VERSION); # else fprintf(STDOUT, "\n\n\nWELCOME TO TREE-PUZZLE %s%s!\n\n\n\n", VERSION, ALPHA); # endif /* vectors used in QP and LM analysis */ qweight = new_dvector(3); sqdiff = new_dvector(3); qworder = new_ivector(3); sqorder = new_ivector(3); /**************************************/ /*** pre-calculations of parameters ***/ /**************************************/ /* Initialization and parsing of Commandline */ setdefaults(); scancmdline(argc, argv); /* initialize random numbers generator */ if (randseed >= 0) fprintf(stderr, "WARNING: random seed set to %d for debugging!\n", randseed); randseed = initrandom(randseed); fprintf(STDOUT, "RANDOM SEED: %d\n", randseed); psteptreelist = NULL; psteptreesum = 0; bestratefound = 0; /* get sequences */ reset = openfiletoread(&seqfp, INFILE, "sequence data"); #if 0 fprintf(stderr, "INFILE=%s\n", INFILE); #endif if (reset && (setprefix_optn < SETPREFIX_INTREE)) { setprefix_optn = SETPREFIX_INFILE; setfilenames(setprefix_optn, RESET_INFILE, INFILE); } /* XXX INFILE */ readsequencefile(seqfp, &Maxspc, &Maxseqc, &Identif, &Namestr, &Seqchars); fprintf(STDOUT, "\nInput data set (%s) contains %d sequences of length %d\n", INFILE, Maxspc, Maxseqc); Maxbrnch = 2*Maxspc - 3; /* output taxa to STDOUT */ for (taxon = 0; taxon < Maxspc; taxon++) { fprintf(stdout, "%4d. ", taxon+1); fputid(stdout, taxon); fprintf(stdout, "\n"); } /* for taxon (species) */ closefile(seqfp); data_optn = guessdatatype(Seqchars, Maxspc, Maxseqc); /* translate characters into format used by ML engine */ nuc_optn = TRUE; SH_optn = FALSE; Seqchar = NULL; translatedataset(Maxspc, Maxseqc, &Maxsite, Seqchars, &Seqchar, &Seqgapchar, &Seqotherchar); /* estimate base frequencies from data set */ Freqtpm = NULL; Basecomp = NULL; estimatebasefreqs(); /* guess model of substitution */ guessmodel(); /* initialize guess variables */ auto_datatype = AUTO_GUESS; if (data_optn == AMINOACID) auto_aamodel = AUTO_GUESS; else auto_aamodel = AUTO_DEFAULT; /* save guessed amino acid options */ guessDayhf_optn = Dayhf_optn; guessJtt_optn = Jtt_optn; guessmtrev_optn = mtrev_optn; guesscprev_optn = cprev_optn; guessblosum62_optn = blosum62_optn; guessvtmv_optn = vtmv_optn; guesswag_optn = wag_optn; guessauto_aamodel = auto_aamodel; /* check for user specified tree */ if ((utfp = fopen(INTREE, "r")) != NULL) { fclose(utfp); if (! consensus_optn) puzzlemode = USERTREE; else puzzlemode = CONSENSUS; } else { puzzlemode = QUARTPUZ; } /* reserve memory for cluster LM analysis */ clusterA = new_ivector(Maxspc); clusterB = new_ivector(Maxspc); clusterC = new_ivector(Maxspc); clusterD = new_ivector(Maxspc); /**********************************/ /*** menu setting of parameters ***/ /**********************************/ /* set options interactively */ setoptions(); /* open usertree file right after start */ if (typ_optn == TREERECON_OPTN && (puzzlemode == USERTREE || puzzlemode == CONSENSUS)) { openfiletoread(&utfp, INTREE, "user trees"); if (reset && (setprefix_optn < SETPREFIX_PREFIX)) { setprefix_optn = SETPREFIX_INTREE; setfilenames(setprefix_optn, RESET_INTREE, INTREE); } /* XXX INFILE */ } /* start main timer */ time(&Starttime); Startcpu=clock(); addtimes(OPTIONS, &tarr); /* symmetrize doublet frequencies if specified */ symdoublets(); /* initialise ML */ mlstart(); /* determine how many usertrees */ if (typ_optn == TREERECON_OPTN && (puzzlemode == USERTREE || puzzlemode == CONSENSUS)) { numutrees = 0; do { ci = fgetc(utfp); if ((char) ci == ';') numutrees++; } while (ci != EOF); rewind(utfp); if (numutrees < 1) { fprintf(STDOUT, "Unable to proceed (no tree in input tree file)\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } } /*epe PP_SendSizes ()/SendData() relocated*/ # if PARALLEL # ifndef USE_WINDOWS PP_SendSizes(Maxspc, Maxsite, numcats, Numptrn, tpmradix, outgroup, fracconst, randseed, fixedorder_optn, consensus_optn); # else PP_SendSizes(Maxspc, Maxsite, alimaxsite, alistart, aliend, numcats, Numptrn, tpmradix, outgroup, fracconst, randseed, fixedorder_optn, consensus_optn); # endif PP_SendData(Seqpat, /* cmatrix */ Alias, Weight, constpat, /* ivector */ Rates, Eval, Freqtpm, /* dvector */ Evec, Ievc, iexp, /* Distanmat,*/ /* dmatrix */ ltprobr); /* dcube */ PP_NoUpdate(); # endif /* PARALLEL */ addtimes(GENERAL, &tarr); time(&PEstStarttime); # ifdef PRINTTIME_DEBUG fprintftimespan(stdout, Starttime, PEstStarttime, Starttime, "Start -> PEst"); # endif /* PRINTTIME_DEBUG */ /*moved from mlstart by epe*/ /* computing ML distances */ computedistan(); #ifdef EPE_DEBUG /*epe*/ for (i=1; i MAXFI) fracinv = MAXFI; addtimes(GENERAL, &tarr); time(&PEstStarttime); # ifdef DEBUG_PRINTTIMES fprintftimespan(stdout, Starttime, PEstStarttime, Starttime, "Start -> PEst"); # endif /* DEBUG_PRINTTIMES */ /***************************/ /*** estimate parameters ***/ /***************************/ if (!(typ_optn == TREERECON_OPTN && (puzzlemode == USERTREE || puzzlemode == CONSENSUS))) { /* no tree present */ estimateparametersnotree(); } else { if (utree_optn) { /* use 1st user tree */ readusertree(utfp, usebranch_optn); rewind(utfp); estimateparameterstree(); } else { /* don't use first user tree */ estimateparametersnotree(); } } time(&PEstStoptime); # ifdef PRINTTIME_DEBUG fprintftimespan(stdout, PEstStarttime, PEstStoptime, Starttime, "PEst"); # endif /* PRINTTIME_DEBUG */ addtimes(PARAMEST, &tarr); /* compute expected Ts/Tv ratio */ if (data_optn == NUCLEOTIDE) computeexpectations(); /*epe*/ # if PARALLEL PP_Final_Update(); # endif /* free_ivector(Seqgapchar); */ /* free_ivector(Seqotherchar); */ } /* inputandinit */ /***************************************************************/ void evaluatetree(FILE *intreefp, FILE *outtreefp, int pmode, int utreenum, int maxutree, int *oldlocroot) /* FILE *intreefp, - file to read tree(s) from */ /* FILE *outtreefp, - file to write result to */ /* int pmode, - analysis type: QUARTPUZ/USERTREE */ /* int utreenum, - current tree number */ /* int maxutree, - amount of trees to analyse */ /* int *oldlocroot - root location for clock analysis */ { switch (pmode) { case QUARTPUZ: /* read QP tree */ readusertree(intreefp, usebranch_optn); fprintf(STDOUT, "Computing maximum likelihood branch lengths (without clock)\n"); fflush(STDOUT); /* pre-set branchlen = FALSE; parallel estim = FALSE */ usertree_lklhd(FALSE, FALSE); /* for savesitelh_optn */ allsitelkl(Ctree->condlkl, allsites[0]); if (rhetmode != UNIFORMRATE) { findbestratecombination(); } break; case USERTREE: /* read user tree */ readusertree(intreefp, usebranch_optn); fprintf(STDOUT, "Computing maximum likelihood branch lengths (without clock) for tree # %d\n", utreenum+1); fflush(STDOUT); /* pre-set branchlen = TRUE; parallel estim = FALSE */ if (usebranch_optn) usertree_lklhd(TRUE, FALSE); /* pre-set branchlen = FALSE; parallel estim = FALSE */ else usertree_lklhd(FALSE, FALSE); if (maxutree > 1) { ulkl[utreenum] = Ctree->lklhd; allsitelkl(Ctree->condlkl, allsites[utreenum]); } else { /* if maxutree == 1 */ /* for savesitelh_optn */ allsitelkl(Ctree->condlkl, allsites[0]); } if ((utreenum==0) && (rhetmode != UNIFORMRATE)) { findbestratecombination(); } break; } /* switch (pmode) */ if (compclock) { /* clocklike branch length */ switch (pmode) { case QUARTPUZ: fprintf(STDOUT, "Computing maximum likelihood branch lengths (with clock)\n"); fflush(STDOUT); break; case USERTREE: fprintf(STDOUT, "Computing maximum likelihood branch lengths (with clock) for tree # %d\n", utreenum+1); fflush(STDOUT); break; } /* find best place for root */ /* default user-set root */ rootsearch = ROOT_USER; /* save or reset the default (user set or -1) */ if ((pmode == USERTREE) && (utreenum > 0)) { /* user trees >1 */ locroot = *oldlocroot; } else { /* 1st user tree or reconstructed tree */ *oldlocroot = locroot; } if (locroot < 0) { /* not set (-1) -> automatic */ locroot = findrootedge(); rootsearch = ROOT_AUTO; } /* if user-specified edge for root does not exist use */ /* displayed outgroup */ if (!checkedge(locroot)) { locroot = outgroup; rootsearch = ROOT_DISPLAYED; } /* compute likelihood */ clock_lklhd(locroot); if (maxutree > 1) { ulklc[utreenum] = Ctree->lklhdc; allsitelkl(Ctree->condlkl, allsitesc[utreenum]); } else { /* if maxutree == 1 */ /* for savesitelh_optn */ allsitelkl(Ctree->condlkl, allsitesc[0]); } } /* write ML branch length tree to outree file */ clockmode = 0; /* nonclocklike branch lengths */ fprintf(outtreefp, "[ lh=%.6f ]", Ctree->lklhd); fputphylogeny(outtreefp); /* clocklike branch lengths */ if (compclock) { clockmode = 1; fprintf(outtreefp, "[ lh=%.6f ]", Ctree->lklhdc); fputrooted(outtreefp, locroot); } fflush(outtreefp); } /* evaluatetree */ /***************************************************************/ void memcleanup() { if (puzzlemode == QUARTPUZ && typ_optn == TREERECON_OPTN) { free(splitfreqs); free(splitpatterns); free(splitsizes); free_ivector(consconfid); free_ivector(conssizes); free_cmatrix(consbiparts); free_ulivector(badtaxon); free_ulimatrix(qinfomatr); if(readsubset_optn) { free_imatrix(ss_setovlgraph); free_imatrix(ss_setoverlaps); free_imatrix(ss_setovllist); free_ivector(ss_setovllistsize); free_imatrix(ss_matrix); free_imatrix(ss_list); free_ivector(ss_listsize); } } free_cmatrix(Identif); free_cmatrix(Namestr); free_dvector(Freqtpm); free_imatrix(Basecomp); free_ivector(clusterA); free_ivector(clusterB); free_ivector(clusterC); free_ivector(clusterD); free_dvector(qweight); free_dvector(sqdiff); free_ivector(qworder); free_ivector(sqorder); freetreelist(&psteptreelist, &psteptreenum, &psteptreesum); freequartets(); } /* memcleanup */ /***************************************************************/ /*** ***/ /*** routines for consensus tree computation ***/ /*** ***/ /***************************************************************/ /* produce consensus from usertrees (onlyconsensus.c) */ /***************************************************************/ /* print i leading spaces to stream fp */ void indent(FILE *fp, int i) { int n; for (n=0; n < i; n++) fputc(' ', fp); } /* indent */ /******************/ /* print speciesnames in leafset (size = setsize) to stream fp */ void printset(FILE *fp, int *leafset, int setsize) { int i; fprintf(fp, "Size=%d: ", setsize); for (i = 0; i < (setsize) ; i++) { fprintf(fp, "%d (", leafset[i]); fputid10(fp, leafset[i]); fprintf(fp, "),"); } fprintf(fp, "\n"); fflush(fp); } /* printset */ /***************************************************************************/ /* copy subtree recursively */ void subtree2bipart(int depth, /* depth from root (for debug) */ cmatrix bip, /* list of bipartitions */ int *numsp, /* number of bipartitions in it */ int *leafset, /* set of leaves in this subtree */ int *setsize, /* size of the set of leaves */ Node *np) /* edge in puzzling step tree */ { int x; int *leafsetr; /* set of leaves in this subtree */ int setsizer; /* size of the set of leaves */ Node *tp; /* test whether we are on an external node */ if (np->isop == NULL) { leafset[(*setsize)] = np->number; (*setsize)++; return; } /* leafsetr = new_ivector(Maxspc); */ setsizer = 0; /* we are NOT on a leaf */ tp = np->isop; while (tp != np) { leafsetr = new_ivector(Maxspc); setsizer = 0; for (x = 0; x < setsizer ; x++) { leafsetr[x]=-1; } subtree2bipart(depth + 1, bip, numsp, leafsetr, &setsizer, tp->kinp); for (x = 0; x < setsizer ; x++) { leafset[(*setsize) + x] = leafsetr[x]; } (*setsize) += setsizer; tp = tp->isop; free_ivector(leafsetr); } if (depth > 1){ for (x = 0; x < (*setsize) ; x++) { bip[*numsp][leafset[x]] = '.'; } # ifdef VERBOSE1 indent(stderr, depth*2); for (x = 0; x < Maxspc ; x++) { fprintf(stderr, "%c", bip[*numsp][x]); } fprintf(stderr, "\n"); # endif /* VERBOSE */ (*numsp)++; } } /* subtree2bipart */ /***************************************************************************/ /* copy treestructure to sorting structure */ void tree2bipart(cmatrix bip, int *numsp) { int *leafset; /* set of leaves in this subtree */ int setsize; /* size of the set of leaves */ int depth; leafset = new_ivector(Maxspc); depth = 0; setsize = 0; /* we are NOT on a leaf */ subtree2bipart(depth + 1, bip, numsp, leafset, &setsize, Ctree->ebrnchp[outgroup]->kinp); free_ivector(leafset); } /* tree2bipart */ /***************************************************************************/ /***************************************************************************/ void usertreeconsensus(FILE* utfp, FILE* outfp, int *oldlocrootptr) { int ci; int i; int n1; int n2; int numsp; FILE *treefp; fprintf(STDOUT, "Performing consensus construction\n"); fflush(STDOUT); numutrees = 0; do { ci = fgetc(utfp); if ((char) ci == ';') numutrees++; } while (ci != EOF); rewind(utfp); if (numutrees < 1) { fprintf(STDOUT, "Unable to proceed (no tree in input tree file)\n\n\n"); exit(1); } /* prepare for consensus tree analysis */ initconsensus(); for (i = 0; i < numutrees; i++) { /* fprintf(stdout, "%d ", i); */ readusertree(utfp, usebranch_optn); for (n1 = 0; n1 < Maxspc - 3; n1++) for (n2 = 0; n2 < Maxspc; n2++) biparts[n1][n2] = '*'; numsp = 0; tree2bipart(biparts, &numsp); makenewsplitentries(biparts, numsp, &splitpatterns, &splitsizes, &splitfreqs, &numbiparts, &maxbiparts, Maxspc); } /* compute majority rule consensus tree */ makeconsensus(numutrees, FALSE); /* write consensus tree */ openfiletowrite(&treefp, TREEFILE, "output tree(s)"); tmpfp = tmpfile(); writeconsensustree(tmpfp, FALSE, qsupportarr); #if 0 if (! skipmlbranch_optn) { #endif if (dotreelh_optn) { rewind(tmpfp); openfiletowrite(&treefp, TREEFILE, "output tree(s)"); evaluatetree(tmpfp, treefp, QUARTPUZ, 0, 1, oldlocrootptr); } else { writeconsensustree(treefp, FALSE, qsupportarr); } closefile(utfp); closefile(treefp); closefile(tmpfp); /* exit(0); */ } /* usertreeconsensus */ /* end onlyconsensus.c */ /******************************************************************************/ /* main part */ /******************************************************************************/ int main(int argc, char *argv[]) { int i, oldlocroot=0; # if !PARALLEL # ifdef USE_CONSOLE argc = ccommand(&argv); # endif # endif /* start main timer */ time(&walltimestart); cputimestart = clock(); inittimearr(&tarr); # if PARALLEL PP_Init(&argc, &argv); if (PP_IamSlave) { slave_main(argc, argv); } else { # endif /* PARALLEL */ inputandinit(&argc, &argv); fprintf(STDOUT, "Writing parameters to file %s\n", OUTFILE); openfiletowrite(&ofp, OUTFILE, "general output"); /* openfiletowrite(&ofp, "xxxx", "general output"); */ writeoutputfile(ofp,WRITEPARAMS); fclose(ofp); /* write distance matrix */ fprintf(STDOUT, "Writing pairwise distances to file %s\n", DISTANCES); openfiletowrite(&dfp, DISTANCES, "pairwise distances"); putdistance(dfp); closefile(dfp); /*epe PP_SendSizes()/SendData() relocated*/ #if 0 # if PARALLEL #ifndef USE_WINDOWS PP_SendSizes(Maxspc, Maxsite, numcats, Numptrn, tpmradix, outgroup, fracconst, randseed, fixedorder_optn, consensus_optn); #else PP_SendSizes(Maxspc, Maxsite, alimaxsite, alistart, aliend, numcats, Numptrn, tpmradix, outgroup, fracconst, randseed, fixedorder_optn, consensus_optn); #endif PP_SendData(Seqpat, /* cmatrix */ Alias, Weight, constpat, /* ivector */ Rates, Eval, Freqtpm, /* dvector */ Evec, Ievc, iexp, Distanmat, /* dmatrix */ ltprobr); /* dcube */ # endif /* PARALLEL */ #endif psteptreestrlen = (Maxspc * (int)(1 + log10((double)Maxspc))) + (Maxspc * 3); switch (typ_optn) { case TREERECON_OPTN: /* tree reconstruction */ if (puzzlemode == QUARTPUZ) { /* quartet puzzling */ recon_tree(); } /* quartet puzzling */ break; case LIKMAPING_OPTN: /* likelihood mapping */ map_lklhd(); break; } /* switch typ_optn */ free_cmatrix(Seqchar); free_cmatrix(Seqchars); /* reserve memory for tree statistics */ if (typ_optn == TREERECON_OPTN) { /* CONSENSUS -> QUARTPUZ, allocates unnecessary memory (HAS) */ if ((puzzlemode == USERTREE) && numutrees > 1) { ulkl = new_dvector(numutrees); allsites = new_dmatrix(numutrees,Numptrn); if (compclock) { ulklc = new_dvector(numutrees); allsitesc = new_dmatrix(numutrees,Numptrn); } } else { /* QUARTPUZ, CONSENSUS */ allsites = new_dmatrix(1,Numptrn); if (compclock) { allsitesc = new_dmatrix(1,Numptrn); } } } /* write puzzling step tree list */ if ((listqptrees == PSTOUT_ORDER) || (listqptrees == PSTOUT_LISTORDER)) { openfiletowrite(&qptorder, OUTPTORDER, "puzzling step trees (unique)"); fprintfsortedpstrees(qptorder, psteptreelist, psteptreenum, psteptreesum, 1, 0.0); closefile(qptorder); } /* compute ML branch lengths for QP tree and for 1st user tree */ switch(typ_optn) { case TREERECON_OPTN: addtimes(GENERAL, &tarr); switch (puzzlemode) { case QUARTPUZ: /* read QP tree */ #if 0 if (! skipmlbranch_optn) { #endif if (dotreelh_optn) { rewind(tmpfp); openfiletowrite(&tfp, TREEFILE, "output tree(s)"); evaluatetree(tmpfp, tfp, puzzlemode, 0, 1, &oldlocroot); addtimes(TREEEVAL, &tarr); closefile(tmpfp); closefile(tfp); } openfiletoappend(&ofp, OUTFILE, "general output"); writeoutputfile(ofp,WRITEREST); break; case USERTREE: /* read user tree */ openfiletoappend(&ofp, OUTFILE, "general output"); openfiletowrite(&tfp, TREEFILE, "output tree(s)"); for (i = 0; i < numutrees; i++) { evaluatetree(utfp, tfp, puzzlemode, i, numutrees, &oldlocroot); if (i==0) writeoutputfile(ofp,WRITEREST); writecutree(ofp, i+1); addtimes(TREEEVAL, &tarr); } closefile(tfp); closefile(utfp); break; case CONSENSUS: /* USERCONSENSUS */ openfiletoappend(&ofp, OUTFILE, "general output"); usertreeconsensus(utfp, ofp, &oldlocroot); /* ends with exit */ openfiletoappend(&ofp, OUTFILE, "general output"); writeoutputfile(ofp,WRITEREST); break; default: /* e.g. distances only */ openfiletoappend(&ofp, OUTFILE, "general output"); writeoutputfile(ofp,WRITEREST); break; } /* switch puzzlemode */ break; default: openfiletoappend(&ofp, OUTFILE, "general output"); writeoutputfile(ofp,WRITEREST); break; } /* switch typ_optn */ /* print tree statistics */ if ((typ_optn == TREERECON_OPTN) && (puzzlemode == USERTREE) && (numutrees > 1) && dotreetest_optn) printtreestats(ofp, ulkl, ulklc, numutrees, allsites, allsitesc, Alias, Maxsite, Numptrn, Weight, compclock); if ((savesitelh_optn || savesitelhb_optn) && (typ_optn == TREERECON_OPTN)) { if (savesitelh_optn) { FILE *outf; openfiletowrite(&outf, SITELH, "write site likelihood"); if (puzzlemode == QUARTPUZ) writesitelklmatrixphy(outf, 1, Maxsite, allsites, allsitesc, compclock); else /* puzzlemode == CONSENSUS ??? */ writesitelklmatrixphy(outf, numutrees, Maxsite, allsites, allsitesc, compclock); fclose(outf); } } /* free memory for tree statistics */ if (typ_optn == TREERECON_OPTN) { if ((puzzlemode == USERTREE || puzzlemode == CONSENSUS) && numutrees > 1) { free_dvector(ulkl); free_dmatrix(allsites); if (compclock) { free_dvector(ulklc); free_dmatrix(allsitesc); } } else { free_dmatrix(allsites); if (compclock) free_dmatrix(allsitesc); } } # if PARALLEL PP_SendDone(); # endif /* PARALLEL */ /* write CPU/Wallclock times and parallel statistics */ time(&walltimestop); cputimestop = clock(); addtimes(OVERALL, &tarr); # ifdef TIMEDEBUG printtimearr(&tarr); # endif /* TIMEDEBUG */ fullcpu = tarr.fullcpu; fulltime = tarr.fulltime; # if PARALLEL writetimesstat(ofp); # endif /* PARALLEL */ /* stop timer */ time(&Stoptime); Stopcpu=clock(); timestamp(ofp); closefile(ofp); /* printbestratecombination(stderr); */ mlfinish(); fprintf(STDOUT, "\nAll results written to disk:\n"); fprintf(STDOUT, " Puzzle report file: %s\n", OUTFILE); fprintf(STDOUT, " Likelihood distances: %s\n", DISTANCES); if (typ_optn == TREERECON_OPTN && puzzlemode != PAIRDIST) fprintf(STDOUT, " Phylip tree file: %s\n", TREEFILE); if (typ_optn == TREERECON_OPTN && puzzlemode == QUARTPUZ) { if ((listqptrees == PSTOUT_ORDER) ||(listqptrees == PSTOUT_LISTORDER)) fprintf(STDOUT, " Unique puzzling step trees: %s\n", OUTPTORDER); if ((listqptrees == PSTOUT_LIST) ||(listqptrees == PSTOUT_LISTORDER)) fprintf(STDOUT, " Puzzling step tree list: %s\n", OUTPTLIST); } if (dotreelh_optn && typ_optn == TREERECON_OPTN && puzzlemode != PAIRDIST) { if (savesitelh_optn) fprintf(STDOUT, " Site likelihoods (PHYLIP): %s\n", SITELH); if (savesitelhb_optn) fprintf(STDOUT, " Site likelihoods (binary): %s\n", SITELHB); if (savesiterate_optn) fprintf(STDOUT, " Site rates (PHYLIP): %s\n", SITERATE); if (savesiterateb_optn) fprintf(STDOUT, " Site rates (binary): %s\n", SITERATEB); } if (show_optn && typ_optn == TREERECON_OPTN && puzzlemode == QUARTPUZ) fprintf(STDOUT, " Unresolved quartets: %s\n", UNRESOLVED); if (typ_optn == LIKMAPING_OPTN) fprintf(STDOUT, " Likelihood mapping diagram: %s\n", TRIANGLE); fprintf(STDOUT, "\n"); # ifdef DEBUG_PRINTTIMES fprintftimespan(stdout, PStepStoptime, Stoptime, Starttime, "Pstep -> end"); # endif /* DEBUG_PRINTTIMES */ /* runtime message */ fprintf(STDOUT, "The parameter estimation took %.2f seconds (= %.2f minutes = %.2f hours)\n", difftime(PEstStoptime, PEstStarttime), difftime(PEstStoptime, PEstStarttime)/60., difftime(PEstStoptime, PEstStarttime)/3600.); fprintf(STDOUT, "The ML step took %.2f seconds (= %.2f minutes = %.2f hours)\n", difftime(MLstepStoptime, MLstepStarttime), difftime(MLstepStoptime, MLstepStarttime)/60., difftime(MLstepStoptime, MLstepStarttime)/3600.); fprintf(STDOUT, "The puzzling step took %.2f seconds (= %.2f minutes = %.2f hours)\n", difftime(PStepStoptime, PStepStarttime), difftime(PStepStoptime, PStepStarttime)/60., difftime(PStepStoptime, PStepStarttime)/3600.); fprintf(STDOUT, "The computation took %.2f seconds (= %.2f minutes = %.2f hours)\n", difftime(Stoptime, Starttime), difftime(Stoptime, Starttime)/60., difftime(Stoptime, Starttime)/3600.); fprintf(STDOUT, " including input %.2f seconds (= %.2f minutes = %.2f hours)\n", fulltime, fulltime/60., fulltime/3600.); #ifdef TIMEDEBUG fprintf(STDOUT, "and %.0f seconds CPU time (= %.2f minutes = %.2f hours)\n\n", fullcpu, fullcpu/60., fullcpu/3600.); #endif /* TIMEDEBUG */ /* free memory */ memcleanup(); # if PARALLEL } /* !IamSlave */ PP_Finalize(); # endif /* PARALLEL */ return 0; } /* main */ /* compare function for uli - sort largest numbers first */ int ulicmp(const void *ap, const void *bp) { uli a, b; a = *((uli *) ap); b = *((uli *) bp); if (a > b) return -1; else if (a < b) return 1; else return 0; } /* ulicmp */ /* compare function for int - sort smallest numbers first */ int intcmp(const void *ap, const void *bp) { int a, b; a = *((int *) ap); b = *((int *) bp); if (a < b) return -1; else if (a > b) return 1; else return 0; } /* intcmp */ tree-puzzle-5.2/src/puzzle2.c0000644000076400001440000015177110074430400011701 /* * puzzle2.c * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifdef HAVE_CONFIG_H # include #endif #define EXTERN extern #include "puzzle.h" #include #if PARALLEL # include "ppuzzle.h" # include "sched.h" #endif /* PARALLEL */ /******************************************************************************/ /* sequences */ /******************************************************************************/ /* read ten characters of current line as identifier */ void readid(FILE *infp, int t) { int i, j, flag, ci; for (i = 0; i < 10; i++) { ci = fgetc(infp); if (ci == EOF || !isprint(ci)) { fprintf(STDOUT, "\n\n\nUnable to proceed (no name for sequence %d)\n\n\n", t+1); # if PARALLEL PP_Finalize(); # endif exit(1); } Identif[t][i] = (char) ci; } /* convert leading blanks in taxon name to underscores */ flag = FALSE; for (i = 9; i > -1; i--) { if (flag == FALSE) { if (Identif[t][i] != ' ') flag = TRUE; } else { if (Identif[t][i] == ' ') Identif[t][i] = '_'; } } /* check whether this name is already used */ for (i = 0; i < t; i++) { /* compare with all other taxa */ flag = TRUE; /* assume identity */ for (j = 0; (j < 10) && (flag == TRUE); j++) if (Identif[t][j] != Identif[i][j]) flag = FALSE; if (flag) { fprintf(STDOUT, "\n\n\nUnable to proceed (multiple occurence of sequence name '"); fputid(STDOUT, t); fprintf(STDOUT, "')\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } } } /* readid */ /******************/ /* read next allowed character */ char readnextcharacter(FILE *ifp, int notu, int nsite) { char c; /* ignore blanks and control characters except newline (UNIX,DOS) or CR (Mac,DOS) */ do { if (fscanf(ifp, "%c", &c) != 1) { fprintf(STDOUT, "\n\n\nUnable to proceed (missing character at position %d in sequence '", nsite + 1); fputid(STDOUT, notu); fprintf(STDOUT, "')\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } } while (c == ' ' || (iscntrl((int) c) && (c != '\n') && (c != '\r'))); return c; } /* readnextcharacter */ /******************/ /* skip rest of the line */ void skiprestofline(FILE *ifp, /* input file stream */ int notu, /* taxon number - for error msg. */ int nsite) /* sequence position - for error msg. */ { int ci; /* read chars until the first newline or CR */ do{ ci = fgetc(ifp); if (ci == EOF) { fprintf(STDOUT, "Unable to proceed (missing newline at position %d in sequence '", nsite + 1); fputid(STDOUT, notu); fprintf(STDOUT, "')\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } } while (((char) ci != '\n') && ((char) ci != '\r')); } /* skiprestofline */ /******************/ /* skip control characters and blanks */ void skipcntrl(FILE *ifp, /* input file stream */ int notu, /* taxon number - for error msg. */ int nsite) /* sequence position - for error msg. */ { int ci; /* read over all control characters and blanks */ do { ci = fgetc(ifp); if (ci == EOF) { fprintf(STDOUT, "\n\n\nUnable to proceed (missing character at position %d in sequence '", nsite + 1); fputid(STDOUT, notu); fprintf(STDOUT, "')\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } } while (iscntrl(ci) || (char) ci == ' '); /* go one character back */ if (ungetc(ci, ifp) == EOF) { fprintf(STDOUT, "\n\n\nUnable to proceed (positioning error at position %d in sequence '", nsite + 1); fputid(STDOUT, notu); fprintf(STDOUT, "')\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } } /* skipcntrl */ /******************/ /* read sequences of one data set */ void getseqs(FILE *ifp, /* in: input file stream */ int Maxspc, /* in: number of taxa */ int Maxseqc, /* in: number of sites */ cmatrix *seqch, /* out: alignment matrix */ cmatrix identif) /* io: taxon names (10 char w/o stop) */ { int notu, nsite, endofline, linelength, i; char c; cmatrix seqchars; seqchars = new_cmatrix(Maxspc, Maxseqc); /* read all characters */ nsite = 0; /* next site to be read */ while (nsite < Maxseqc) { /* read first taxon */ notu = 0; /* only Maxspc, Maxseqc read so far: */ /* go to next true line */ skiprestofline(ifp, notu, nsite); skipcntrl(ifp, notu, nsite); if (nsite == 0) readid(ifp, notu); endofline = FALSE; linelength = 0; do { c = readnextcharacter(ifp, notu, nsite + linelength); if ((c == '\n') || (c == '\r')) endofline = TRUE; else if (c == '.') { fprintf(STDOUT, "\n\n\nUnable to proceed (invalid character '.' at position "); fprintf(STDOUT, "%d in first sequence)\n\n\n", nsite + linelength + 1); # if PARALLEL PP_Finalize(); # endif exit(1); } else if (nsite + linelength < Maxseqc) { /* change to upper case */ seqchars[notu][nsite + linelength] = (char) toupper((int) c); linelength++; } else { endofline = TRUE; skiprestofline(ifp, notu, nsite + linelength); } } while (!endofline); if (linelength == 0) { fprintf(STDOUT, "\n\n\nUnable to proceed (line with length 0 at position %d in sequence '", nsite + 1); fputid(STDOUT, notu); fprintf(STDOUT, "')\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } /* read other taxa */ for (notu = 1; notu < Maxspc; notu++) { /* go to next true line */ if (notu != 1) skiprestofline(ifp, notu, nsite); skipcntrl(ifp, notu, nsite); if (nsite == 0) readid(ifp, notu); for (i = nsite; i < nsite + linelength; i++) { c = readnextcharacter(ifp, notu, i); if ((c == '\n') || (c == '\r')) { /* too short */ fprintf(STDOUT, "\n\n\nUnable to proceed (line to short at position %d in sequence '", i + 1); fputid(STDOUT, notu); fprintf(STDOUT, "')\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } else if (c == '.') { seqchars[notu][i] = seqchars[0][i]; } else { /* change to upper case */ seqchars[notu][i] = (char) toupper((int) c); } } } nsite = nsite + linelength; } *seqch =seqchars; } /* getseqs */ /******************/ /* initialize identifer arrays */ void initid(int t, /* in: number of taxa */ cmatrix *identif, /* out: name array w/o end of string */ cmatrix *namestr) /* out: name array with end of string */ { int i, j; *identif = new_cmatrix(t, 10); *namestr = new_cmatrix(t, 11); for (i = 0; i < t; i++) { (*namestr)[i][0] = '\0'; (*namestr)[i][9] = '\0'; for (j = 0; j < 10; j++) { (*identif)[i][j] = ' '; } /* for j */ } /* for i */ } /* initid */ /******************/ /******************/ /* copy undelimited identifer array to '\0' delimited identifer array */ void identif2namestr(int num, /* number of taxa */ cmatrix Identif, /* non-delimited names */ cmatrix Namestr) /* proper delimited names */ { int i, j; int laggingspc; for (i = 0; i < num; i++) { laggingspc = 1; for (j = 9; j >= 0; j--) { Namestr[i][j] = Identif[i][j]; if (laggingspc == 1) { if (Identif[i][j] != ' ') { Namestr[i][j+1] = '\0'; laggingspc = 0; } } } /* for j (letter 10-1) */ } /* for i (species) */ } /* identif2namestr */ /******************/ /* print identifier of specified taxon in full 10 char length */ void fputid10(FILE *ofp, int t) { int i; for (i = 0; i < 10; i++) fputc(Identif[t][i], ofp); } /* fputid10 */ /******************/ /* print identifier of specified taxon up to first space */ int fputid(FILE *ofp, int t) { int i; i = 0; while (i < 10 && Identif[t][i] != ' ') { fputc(Identif[t][i], ofp); i++; } return i; } /* fputid */ /******************/ /* read first line of sequence data set */ void getsizesites(FILE *ifp, /* in: input file stream */ int *Maxspc, /* out: number of taxa */ int *Maxseqc) /* out: number of sites */ { if (fscanf(ifp, "%d", Maxspc) != 1) { fprintf(STDOUT, "\n\n\nUnable to proceed (missing number of sequences)\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } if (fscanf(ifp, "%d", Maxseqc) != 1) { fprintf(STDOUT, "\n\n\nUnable to proceed (missing number of sites)\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } if (*Maxspc < 3) { fprintf(STDOUT, "\n\n\nUnable to proceed (less than 3 sequences - no tree possible)\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } seqnumcheck = SEQNUM_OK; if (*Maxspc < 4) { fprintf(STDOUT, "\n\n\nLess than 4 sequences: No quartet methods possible!!!\n\n\n"); fprintf(STDOUT, "Parameter estimation and tree testing is still possible.\n\n\n"); seqnumcheck = SEQNUM_TOOFEW; } if (*Maxspc > 257) { fprintf(STDOUT, "\n\n\nMore than 257 sequences: No quartet puzzling available!!!\n"); fprintf(STDOUT, "Parameter estimation, likelihood mapping, and tree testing is still possible.\n\n\n"); seqnumcheck = SEQNUM_TOOMANY; } /* correct default analysis types */ if ((seqnumcheck!=SEQNUM_OK) && (puzzlemode==QUARTPUZ)) puzzlemode = (puzzlemode + 1) % NUMPUZZLEMODES; if ((seqnumcheck==SEQNUM_TOOFEW) && (typ_optn==LIKMAPING_OPTN)) typ_optn = (typ_optn + 1) % NUMTYPES; #if 0 if (*Maxspc < 4) { fprintf(STDOUT, "\n\n\nUnable to proceed (less than 4 sequences)\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } if (*Maxspc > 257) { fprintf(STDOUT, "\n\n\nUnable to proceed (more than 257 sequences)\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } # endif if (*Maxseqc < 1) { fprintf(STDOUT, "\n\n\nUnable to proceed (no sequence sites)\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } } /* getsizesites */ /******************/ /* read alignment from file */ void readsequencefile(FILE *seqfp, /* in: sequence input file stream */ int *Maxspc, /* out: number of taxa */ int *Maxseqc, /* out: number of sites */ cmatrix *identif, /* out: name array w/o end of str */ cmatrix *namestr, /* out: name array with end of str */ cmatrix *Seqchars) /* out: alignment matrix */ { getsizesites(seqfp, Maxspc, Maxseqc); initid(*Maxspc, identif, namestr); getseqs(seqfp, *Maxspc, *Maxseqc, Seqchars, *identif); identif2namestr(*Maxspc, *identif, *namestr); } /* readsequencefile */ /******************/ /* read subsets from file */ void readsubsetfile(FILE *seqfp, /* in: sequence input file stream */ int Maxspc, /* in: number of taxa */ cmatrix namestr, /* in: names taxa (seq file) */ int *Maxsubset, /* out: number of subsets */ imatrix *ss_setovlgraph, /* out: size of overlap >= 3 between 2 subsets */ imatrix *ss_setoverlaps, /* out: size of overlap between 2 subsets */ imatrix *ss_setovllist, /* out: list with ovlerlapping subsets */ ivector *ss_setovllistsize, /* out: size of list with ovlerlapping subsets */ imatrix *ss_matrix, /* out: boolean list: taxon in set? */ imatrix *ss_list, /* out: list of taxa in set */ ivector *ss_listsize) /* out: size of list with taxa */ { int ss_maxspc; int n; int set1, set2; int tmp; cmatrix ss_identarr; cmatrix ss_namearr; cmatrix ss_strmatr; /* read the subset file sizes */ getsizesites(seqfp, &ss_maxspc, Maxsubset); /* check sizes */ if (ss_maxspc != Maxspc) { fprintf(STDOUT, "ERROR: Number of taxa in subsetfile does not match!!! (%d != %d)\n", ss_maxspc, Maxspc); # if PARALLEL PP_SendDone(); MPI_Finalize(); # endif /* PARALLEL */ exit(1); } /* initialize name arrays for checking */ initid(ss_maxspc, &ss_identarr, &ss_namearr); /* read the data */ getseqs(seqfp, ss_maxspc, *Maxsubset, &ss_strmatr, ss_identarr); /* check the file names */ identif2namestr(ss_maxspc, ss_identarr, ss_namearr); for(n = 0; n= 3) { /* number of sequences (>=3) in overlap */ (*ss_setovlgraph)[set1][set2] = tmp; (*ss_setovlgraph)[set2][set1] = tmp; /* list of overlapping sets */ (*ss_setovllist)[set1][((*ss_setovllistsize)[set1])++] = set2; (*ss_setovllist)[set2][((*ss_setovllistsize)[set2])++] = set1; } } } } /* readsubsetfile */ /******************/ /* permute taxon order */ void permutetaxa_ss(int Maxspc, /* in: number of taxa */ ivector permutation, /* permuted taxon order */ cmatrix namestr, /* in: names taxa (seq file) */ int Maxsubset, /* out: number of subsets */ imatrix ss_setovlgraph, /* out: size of overlap >= 3 between 2 subsets */ imatrix ss_setoverlaps, /* out: size of overlap between 2 subsets */ imatrix ss_setovllist, /* out: list with ovlerlapping subsets */ ivector ss_setovllistsize, /* out: size of list with ovlerlapping subsets */ imatrix ss_matrix, /* out: boolean list: taxon in set? */ imatrix ss_list, /* out: list of taxa in set */ ivector ss_listsize) /* out: size of list with taxa */ { ivector candidatesetlist; int candidatesetsize = 0; ivector candidatetaxalist; int candidatetaxasize = 0; ivector taxonstatus; /* 0 - not done; 1 - candidate; 2 - inserted */ ivector setstatus; /* 0 - not used; 1 - front; 2 - used*/ int permpos; int k; int tmprand; int currset; int currtaxon; candidatesetlist = new_ivector(Maxsubset); candidatetaxalist = new_ivector(Maxspc); taxonstatus = new_ivector(Maxspc); setstatus = new_ivector(Maxsubset); /* first subset */ currset = randominteger(Maxsubset); setstatus[currset] = 2; /* inserted */ /* init subset front nodes */ /* insert sets with ovl(currset) >= 3 into candidate set list */ for (k=0; k=3) to set candidate list */ for (k=0; k= 3 between 2 subsets */ imatrix ss_setoverlaps, /* out: size of overlap between 2 subsets */ imatrix ss_setovllist, /* out: list with ovlerlapping subsets */ ivector ss_setovllistsize, /* out: size of list with ovlerlapping subsets */ imatrix ss_matrix, /* out: boolean list: taxon in set? */ imatrix ss_list, /* out: list of taxa in set */ ivector ss_listsize) /* out: size of list with taxa */ { int s, s1, s2, t; for (s=0; s= 3 between 2 subsets */ imatrix ss_setoverlaps, /* out: size of overlap between 2 subsets */ imatrix ss_setovllist, /* out: list with ovlerlapping subsets */ ivector ss_setovllistsize, /* out: size of list with ovlerlapping subsets */ imatrix ss_matrix, /* out: boolean list: taxon in set? */ imatrix ss_list, /* out: list of taxa in set */ ivector ss_listsize) /* out: size of list with taxa */ { int s1, s2; int numdone; int *setarr; setarr = new_ivector(Maxsubset); s1 = 0; numdone=0; do { setarr[s1] = 2; /* 1=seen, 2=visited */ for (s2=0; s2= 3)) setarr[s2]=1; } numdone++; s1=0; while ((s1 < Maxsubset) && (setarr[s1]!=1)) s1++; } while (s1 != Maxsubset); if (Maxsubset != numdone) { fprintf(stderr, "Unable to proceed. More than one connected component! (%d != %d)\n", Maxsubset, numdone); fprintf(stderr, "visited: \n "); for (s2=0; s2 0.85) return NUCLEOTIDE; /* 0 */ else if ((double) numbins / (double) numchars > 0.2) return BINARY; /* 2 */ else return AMINOACID; /* 1 */ } /* guessdatatype */ /******************/ /* translate characters into format used by ML engine */ void translatedataset(int maxspc, int maxseqc, int *maxsite, cmatrix seqchars, cmatrix *seqchar, ivector *seqgapchar, ivector *seqotherchar) { int notu, sn, co; char c; cvector code; if (*seqgapchar != NULL) free_ivector(*seqgapchar); if (*seqotherchar != NULL) free_ivector(*seqotherchar); Seqgapchar = new_ivector(Maxspc); Seqotherchar = new_ivector(Maxspc); /* Seqgapchar = (int *) calloc(maxspc, sizeof(int)); */ /* Seqotherchar = (int *) calloc(maxspc, sizeof(int)); */ /* determine maxsite - number of ML sites per taxon */ if (data_optn == NUCLEOTIDE && SH_optn) { if (SHcodon) *maxsite = maxseqc / 3; else *maxsite = maxseqc / 2; /* assume doublets */ } else *maxsite = maxseqc; if (data_optn == NUCLEOTIDE && (*maxsite % 3) == 0 && !SH_optn) { if (codon_optn == 1 || codon_optn == 2 || codon_optn == 3) *maxsite = *maxsite / 3; /* only one of the three codon positions */ if (codon_optn == 4) *maxsite = 2*(*maxsite / 3); /* 1st + 2nd codon positions */ } /* reserve memory */ if (*seqchar != NULL) free_cmatrix(*seqchar); *seqchar = new_cmatrix(maxspc, *maxsite); /* code length */ if (data_optn == NUCLEOTIDE && SH_optn) code = new_cvector(2); else code = new_cvector(1); /* decode characters */ if (data_optn == NUCLEOTIDE && SH_optn) { /* SH doublets */ for (notu = 0; notu < maxspc; notu++) { for (sn = 0; sn < *maxsite; sn++) { for (co = 0; co < 2; co++) { if (SHcodon) c = seqchars[notu][sn*3 + co]; else c = seqchars[notu][sn*2 + co]; code[co] = c; } (*seqchar)[notu][sn] = code2int(code, &((*seqgapchar)[notu]), &((*seqotherchar)[notu])); } } } else if (!(data_optn == NUCLEOTIDE && (maxseqc % 3) == 0)) { /* use all */ for (notu = 0; notu < maxspc; notu++) { for (sn = 0; sn < *maxsite; sn++) { code[0] = seqchars[notu][sn]; (*seqchar)[notu][sn] = code2int(code, &((*seqgapchar)[notu]), &((*seqotherchar)[notu])); } } } else { /* codons */ for (notu = 0; notu < maxspc; notu++) { for (sn = 0; sn < *maxsite; sn++) { if (codon_optn == 1 || codon_optn == 2 || codon_optn == 3) code[0] = seqchars[notu][sn*3+codon_optn-1]; else if (codon_optn == 4) { if ((sn % 2) == 0) code[0] = seqchars[notu][(sn/2)*3]; else code[0] = seqchars[notu][((sn-1)/2)*3+1]; } else code[0] = seqchars[notu][sn]; (*seqchar)[notu][sn] = code2int(code, &((*seqgapchar)[notu]), &((*seqotherchar)[notu])); } } } free_cvector(code); } /* translatedataset */ /******************/ /* estimate mean base frequencies from translated data set */ void estimatebasefreqs() { int tpmradix, i, j; uli all, *gene; tpmradix = gettpmradix(); if (Freqtpm != NULL) free_dvector(Freqtpm); Freqtpm = new_dvector(tpmradix); if (Basecomp != NULL) free_imatrix(Basecomp); Basecomp = new_imatrix(Maxspc, tpmradix); gene = (uli *) calloc((size_t) (tpmradix + 1), sizeof(uli)); if (gene == NULL) maerror("gene in estimatebasefreqs"); for (i = 0; i < tpmradix + 1; i++) gene[i] = 0; for (i = 0; i < Maxspc; i++) for (j = 0; j < tpmradix; j++) Basecomp[i][j] = 0; for (i = 0; i < Maxspc; i++) for (j = 0; j < Maxsite; j++) { gene[(int) Seqchar[i][j]]++; if (Seqchar[i][j] != tpmradix) Basecomp[i][(int) Seqchar[i][j]]++; } all = Maxspc * Maxsite - gene[tpmradix]; if (all != 0) { /* normal case */ for (i = 0; i < tpmradix; i++) Freqtpm[i] = (double) gene[i] / (double) all; } else { /* pathological case with no unique character in data set */ for (i = 0; i < tpmradix; i++) Freqtpm[i] = 1.0 / (double) tpmradix; } free(gene); Frequ_optn = TRUE; } /* estimatebasefreqs */ /******************/ /* guess model of substitution */ void guessmodel() { double c1, c2, c3, c4, c5, c6; dvector f; dmatrix a; int i; Dayhf_optn = FALSE; Jtt_optn = TRUE; mtrev_optn = FALSE; cprev_optn = FALSE; blosum62_optn = FALSE; vtmv_optn = FALSE; wag_optn = FALSE; TSparam = 2.0; YRparam = 1.0; optim_optn = TRUE; HKY_optn = TRUE; print_GTR_optn = TRUE; GTR_optn = FALSE; TN_optn = FALSE; if (data_optn == AMINOACID) { /* amino acids */ /* chi2 fit to amino acid frequencies */ f = new_dvector(20); a = new_dmatrix(20,20); /* chi2 distance Dayhoff */ dyhfdata(a, f); c1 = 0; for (i = 0; i < 20; i++) c1 = c1 + (Freqtpm[i]-f[i])*(Freqtpm[i]-f[i]); /* chi2 distance JTT */ jttdata(a, f); c2 = 0; for (i = 0; i < 20; i++) c2 = c2 + (Freqtpm[i]-f[i])*(Freqtpm[i]-f[i]); /* chi2 distance mtREV */ mtrevdata(a, f); c3 = 0; for (i = 0; i < 20; i++) c3 = c3 + (Freqtpm[i]-f[i])*(Freqtpm[i]-f[i]); /* chi2 distance VT */ vtmvdata(a, f); c4 = 0; for (i = 0; i < 20; i++) c4 = c4 + (Freqtpm[i]-f[i])*(Freqtpm[i]-f[i]); /* chi2 distance WAG */ wagdata(a, f); c5 = 0; for (i = 0; i < 20; i++) c5 = c5 + (Freqtpm[i]-f[i])*(Freqtpm[i]-f[i]); /* chi2 distance cpREV */ cprev45data(a, f); c6 = 0; for (i = 0; i < 20; i++) c6 = c6 + (Freqtpm[i]-f[i])*(Freqtpm[i]-f[i]); free_dvector(f); free_dmatrix(a); #ifndef CPREV if ((c1 < c2) && (c1 < c3) && (c1 < c4) && (c1 < c5)) { /* c1 -> Dayhoff */ Dayhf_optn = TRUE; Jtt_optn = FALSE; mtrev_optn = FALSE; cprev_optn = FALSE; vtmv_optn = FALSE; wag_optn = FALSE; fprintf(STDOUT, "(consists very likely of amino acids encoded on nuclear DNA)\n"); } else { if ((c2 < c3) && (c2 < c4) && (c2 < c5)) { /* c2 -> JTT */ Dayhf_optn = FALSE; Jtt_optn = TRUE; mtrev_optn = FALSE; cprev_optn = FALSE; vtmv_optn = FALSE; wag_optn = FALSE; fprintf(STDOUT, "(consists very likely of amino acids encoded on nuclear DNA)\n"); } else { if ((c3 < c4) && (c3 < c5)) { /* c3 -> mtREV */ Dayhf_optn = FALSE; Jtt_optn = FALSE; mtrev_optn = TRUE; cprev_optn = FALSE; vtmv_optn = FALSE; wag_optn = FALSE; fprintf(STDOUT, "(consists very likely of amino acids encoded on mtDNA)\n"); } else { if ((c4 < c5)) { /* c4 -> VT */ Dayhf_optn = FALSE; Jtt_optn = FALSE; mtrev_optn = FALSE; cprev_optn = FALSE; vtmv_optn = TRUE; wag_optn = FALSE; fprintf(STDOUT, "(consists very likely of amino acids encoded on nuclear DNA)\n"); } else { /* c5 -> WAG */ Dayhf_optn = FALSE; Jtt_optn = FALSE; mtrev_optn = FALSE; cprev_optn = FALSE; vtmv_optn = FALSE; wag_optn = TRUE; fprintf(STDOUT, "(consists very likely of amino acids encoded on nuclear DNA)\n"); } /* if c4 else c5 */ } /* if c3 else c4 */ } /* if c2 */ } /* if c1 */ #else /* CPREV */ if ((c1 < c2) && (c1 < c3) && (c1 < c4) && (c1 < c5) && (c1 < c6)) { /* c1 -> Dayhoff */ Dayhf_optn = TRUE; Jtt_optn = FALSE; mtrev_optn = FALSE; cprev_optn = FALSE; vtmv_optn = FALSE; wag_optn = FALSE; fprintf(STDOUT, "(consists very likely of amino acids encoded on nuclear DNA)\n"); } else { if ((c2 < c3) && (c2 < c4) && (c2 < c5) && (c2 < c6)) { /* c2 -> JTT */ Dayhf_optn = FALSE; Jtt_optn = TRUE; mtrev_optn = FALSE; cprev_optn = FALSE; vtmv_optn = FALSE; wag_optn = FALSE; fprintf(STDOUT, "(consists very likely of amino acids encoded on nuclear DNA)\n"); } else { if ((c3 < c4) && (c3 < c5) && (c3 < c6)) { /* c3 -> mtREV */ Dayhf_optn = FALSE; Jtt_optn = FALSE; mtrev_optn = TRUE; cprev_optn = FALSE; vtmv_optn = FALSE; wag_optn = FALSE; fprintf(STDOUT, "(consists very likely of amino acids encoded on mtDNA)\n"); } else { if ((c4 < c5) && (c4 < c6)) { /* c4 -> VT */ Dayhf_optn = FALSE; Jtt_optn = FALSE; mtrev_optn = FALSE; cprev_optn = FALSE; vtmv_optn = TRUE; wag_optn = FALSE; fprintf(STDOUT, "(consists very likely of amino acids encoded on nuclear DNA)\n"); } else { if (c5 < c6) { /* c5 -> WAG */ Dayhf_optn = FALSE; Jtt_optn = FALSE; mtrev_optn = FALSE; cprev_optn = FALSE; vtmv_optn = FALSE; wag_optn = TRUE; fprintf(STDOUT, "(consists very likely of amino acids encoded on nuclear DNA)\n"); } else { /* if (c6) */ /* c6 -> cpREV */ Dayhf_optn = FALSE; Jtt_optn = FALSE; mtrev_optn = FALSE; cprev_optn = TRUE; vtmv_optn = FALSE; wag_optn = FALSE; fprintf(STDOUT, "(consists very likely of amino acids encoded on cpDNA)\n"); } /* if c5 else c6 */ } /* if c4 else c5 */ } /* if c3 else c4 */ } /* if c2 */ } /* if c1 */ #endif /* CPREV */ } else if (data_optn == NUCLEOTIDE) { fprintf(STDOUT, "(consists very likely of nucleotides)\n"); } else { fprintf(STDOUT, "(consists very likely of binary state data)\n"); } } /* guessmodel */ /******************************************************************************/ /* parts outsourced to treesort.c/treesort.h */ #if 0 /* TREESORT_H */ #endif /* TREESORT_H */ /* parts outsourced to consensus.c/consensus.h */ #if 0 /* CONSENSUS_H */ #endif /* CONSENSUS_H */ /******************************************************************************/ /* storing and evaluating quartet branching information */ /******************************************************************************/ /* general remarks: for a quartet with the taxa a, b, c, d there are three possible binary trees: 1) (a,b)-(c,d) 2) (a,c)-(b,d) 3) (a,d)-(b,c) For every quartet information about its branching structure is stored. With the functions readquartet and writequartet this information can be accessed. For every quartet (a,b,c,d) with a < b < c < d (taxa) the branching information is encoded using 4 bits: value 8 4 2 1 +-------------+-------------+-------------+-------------+ | not used | tree 3 | tree 2 | tree 1 | +-------------+-------------+-------------+-------------+ If the branching structure of the taxa corresponds to one of the three trees the corresponding bit is set. If the branching structure is unclear because two of the three trees have the same maximum likelihood value the corresponding two bits are set. If the branching structure is completely unknown all the bits are set (the highest bit is always cleared because it is not used). */ /* allocate memory for quartets */ unsigned char *callocquartets(int taxa) { uli nc, numch; unsigned char *qinfo; /* compute number of quartets */ Numquartets = (uli) taxa*(taxa-1)*(taxa-2)*(taxa-3)/24; if (Numquartets % 2 == 0) { /* even number */ numch = Numquartets/2; } else { /* odd number */ numch = (Numquartets + 1)/2; } /* allocate memory */ qinfo = (unsigned char *) calloc((size_t) numch, sizeof(unsigned char)); if (qinfo == NULL) maerror("quartetinfo in callocquartets"); for (nc = 0; nc < numch; nc++) qinfo[nc] = 0; return(qinfo); } /* callocquartets */ /* free quartet memory */ void freequartets() { free(quartetinfo); } /* freequartets */ /**************/ /* read quartet info - a < b < c < d */ unsigned char readquartet(int a, int b, int c, int d) { uli qnum; if (! ((a < b) && (b < c) && (c < d))) { fprintf(stderr, "\n\n\nHALT: PLEASE REPORT ERROR HS2 TO DEVELOPERS! (%d,%d,%d,%d)\n", a,b,c,d); # if PARALLEL PP_Finalize(); # endif exit (999); } qnum = (uli) a + (uli) b*(b-1)/2 + (uli) c*(c-1)*(c-2)/6 + (uli) d*(d-1)*(d-2)*(d-3)/24; if (qnum % 2 == 0) { /* even number */ /* bits 0 to 3 */ return (quartetinfo[qnum/2] & (unsigned char) 15); } else { /* odd number */ /* bits 4 to 7 */ return ((quartetinfo[(qnum-1)/2] & (unsigned char) 240)>>4); } } /* readquartet */ /**************/ /* write quartet info - a < b < c < d, 0 <= info <= 15 */ void writequartet(int a, int b, int c, int d, unsigned char info) { uli qnum; qnum = (uli) a + (uli) b*(b-1)/2 + (uli) c*(c-1)*(c-2)/6 + (uli) d*(d-1)*(d-2)*(d-3)/24; if (qnum % 2 == 0) { /* even number */ /* bits 0 to 3 */ quartetinfo[qnum/2] = ((quartetinfo[qnum/2] & (unsigned char) 240) | (info & (unsigned char) 15)); } else { /* odd number */ /* bits 4 to 7 */ quartetinfo[(qnum-1)/2] = ((quartetinfo[(qnum-1)/2] & (unsigned char) 15) | ((info & (unsigned char) 15)<<4)); } } /* writequartet */ /**************/ /* prototypes */ int openfiletowrite(FILE **, char[], char[]); void closefile(FILE *); /* sorts three doubles in descending order */ void sort3doubles(dvector num, ivector order) { if (num[0] > num[1]) { if(num[2] > num[0]) { order[0] = 2; order[1] = 0; order[2] = 1; } else if (num[2] < num[1]) { order[0] = 0; order[1] = 1; order[2] = 2; } else { order[0] = 0; order[1] = 2; order[2] = 1; } } else { if(num[2] > num[1]) { order[0] = 2; order[1] = 1; order[2] = 0; } else if (num[2] < num[0]) { order[0] = 1; order[1] = 0; order[2] = 2; } else { order[0] = 1; order[1] = 2; order[2] = 0; } } } /* sort3doubles */ /*************************/ /* compute Bayesian weights from log-lkls d1, d2, d3 */ unsigned char loglkl2weight(int a, int b, int c, int i, double d1, double d2, double d3, int usebestq) { double onethird; unsigned char treebits[3]; double templog; unsigned char tmpweight; double temp; double temp1, temp2, temp3; unsigned char discreteweight[3]; double tttqweight[3]; double tttsqdiff[3]; int tttsqorder[3]; int tttqworder[3]; tttqweight[0] = d1; tttqweight[1] = d2; tttqweight[2] = d3; onethird = 1.0/3.0; treebits[0] = (unsigned char) 1; treebits[1] = (unsigned char) 2; treebits[2] = (unsigned char) 4; /* sort in descending order */ sort3doubles(tttqweight, tttqworder); if (usebestq) { tttsqorder[2] = 2; discreteweight[tttsqorder[2]] = treebits[tttqworder[0]]; if (tttqweight[tttqworder[0]] == tttqweight[tttqworder[1]]) { discreteweight[tttsqorder[2]] = discreteweight[tttsqorder[2]] || treebits[tttqworder[1]]; if (tttqweight[tttqworder[1]] == tttqweight[tttqworder[2]]) { discreteweight[tttsqorder[2]] = discreteweight[tttsqorder[2]] || treebits[tttqworder[2]]; discreteweight[tttsqorder[2]] = 7; } } } else { /* compute Bayesian weights */ templog = tttqweight[tttqworder[1]]-tttqweight[tttqworder[0]]; if(templog < -TP_MAX_EXP_DIFF) /* possible, since 1.0+exp(>36) == 1.0 */ tttqweight[tttqworder[1]] = 0.0; else tttqweight[tttqworder[1]] = exp(templog); templog = tttqweight[tttqworder[2]]-tttqweight[tttqworder[0]]; if(templog < -TP_MAX_EXP_DIFF) /* possible, since 1.0+exp(>36) == 1.0 */ tttqweight[tttqworder[2]] = 0.0; else tttqweight[tttqworder[2]] = exp(templog); tttqweight[tttqworder[0]] = 1.0; temp = tttqweight[0] + tttqweight[1] + tttqweight[2]; tttqweight[0] = tttqweight[0]/temp; tttqweight[1] = tttqweight[1]/temp; tttqweight[2] = tttqweight[2]/temp; /* square deviations */ temp1 = 1.0 - tttqweight[tttqworder[0]]; tttsqdiff[0] = temp1 * temp1 + tttqweight[tttqworder[1]] * tttqweight[tttqworder[1]] + tttqweight[tttqworder[2]] * tttqweight[tttqworder[2]]; discreteweight[0] = treebits[tttqworder[0]]; temp1 = 0.5 - tttqweight[tttqworder[0]]; temp2 = 0.5 - tttqweight[tttqworder[1]]; tttsqdiff[1] = temp1 * temp1 + temp2 * temp2 + tttqweight[tttqworder[2]] * tttqweight[tttqworder[2]]; discreteweight[1] = treebits[tttqworder[0]] + treebits[tttqworder[1]]; temp1 = onethird - tttqweight[tttqworder[0]]; temp2 = onethird - tttqweight[tttqworder[1]]; temp3 = onethird - tttqweight[tttqworder[2]]; tttsqdiff[2] = temp1 * temp1 + temp2 * temp2 + temp3 * temp3; discreteweight[2] = (unsigned char) 7; /* sort in descending order */ sort3doubles(tttsqdiff, tttsqorder); } tmpweight = discreteweight[tttsqorder[2]]; return(tmpweight); } /* loglkl2weight */ /*************************/ /* checks out all possible quartets */ void computeallquartets() { double onethird; uli nq; unsigned char treebits[3]; # if ! PARALLEL unsigned char tmpweight; FILE *lhfp; int a, b, c, i; # endif onethird = 1.0/3.0; treebits[0] = (unsigned char) 1; treebits[1] = (unsigned char) 2; treebits[2] = (unsigned char) 4; if (show_optn) { /* list all unresolved quartets */ openfiletowrite(&unresfp, UNRESOLVED, "unresolved quartet trees"); fprintf(unresfp, "List of all completely unresolved quartets:\n\n"); } nq = 0; badqs = 0; /* start timer - percentage of completed quartets */ time(&time0); time1 = time0; mflag = 0; # if PARALLEL { schedtype sched; int flag; MPI_Status stat; int dest = 1; uli qaddr =0; uli qamount=0; int qblocksent = 0; int apr; uli Sumquartets; uli sq, noq; uli tmpfullresqs; uli tmppartresqs; uli tmpunresqs; uli tmpmissingqs; Sumquartets = numquarts(Maxspc); initsched(&sched, Sumquartets, PP_NumProcs-1, 4); qamount=SCHEDALG_ML_STEP(&sched); while (qamount > 0) { if (PP_emptyslave()) { PP_RecvQuartBlock(0, &sq, &noq, quartetinfo, &tmpfullresqs, &tmppartresqs, &tmpunresqs, &tmpmissingqs, &usebestq_optn, &apr); qblocksent -= noq; } dest = PP_getslave(); PP_SendDoQuartBlock(dest, qaddr, qamount, usebestq_optn, (approxqp ? APPROX : EXACT)); qblocksent += qamount; qaddr += qamount; qamount=SCHEDALG_ML_STEP(&sched); MPI_Iprobe(MPI_ANY_SOURCE, PP_QUARTBLOCKSPECS, PP_Comm, &flag, &stat); while (flag) { PP_RecvQuartBlock(0, &sq, &noq, quartetinfo, &tmpfullresqs, &tmppartresqs, &tmpunresqs, &tmpmissingqs, &usebestq_optn, &apr); qblocksent -= noq; MPI_Iprobe(MPI_ANY_SOURCE, PP_QUARTBLOCKSPECS, PP_Comm, &flag, &stat); } checktime(&time0, &time1, &time2, qaddr - qblocksent, Sumquartets, &mflag); } while (qblocksent > 0) { PP_RecvQuartBlock(0, &sq, &noq, quartetinfo, &tmpfullresqs, &tmppartresqs, &tmpunresqs, &tmpmissingqs, &usebestq_optn, &apr); qblocksent -= noq; checktime(&time0, &time1, &time2, qaddr - qblocksent, Sumquartets, &mflag); } } # else /* ! PARALLEL */ addtimes(GENERAL, &tarr); if (savequartlh_optn) { openfiletowrite(&lhfp, ALLQUARTLH, "all quartet likelihoods"); if (saveqlhbin_optn) writetpqfheader(Maxspc, lhfp, 3); else writetpqfheader(Maxspc, lhfp, 4); } for (i = 3; i < Maxspc; i++) for (c = 2; c < i; c++) for (b = 1; b < c; b++) for (a = 0; a < b; a++) { nq++; /* generate message every >TIMECHECK_INTERVAL seconds */ /* check timer */ checktime(&time0, &time1, &time2, nq, Numquartets, &mflag); /* maximum likelihood values */ /* exact or approximate maximum likelihood values */ compute_quartlklhds(a,b,c,i,&qweight[0],&qweight[1],&qweight[2], (approxqp ? APPROX : EXACT)); if (savequartlh_optn) { if (saveqlhbin_optn) fwrite(qweight, sizeof(double), 3, lhfp); else fprintf(lhfp, "(%d,%d,%d,%d)\t%f\t%f\t%f\n", a, b, c, i, qweight[0], qweight[1], qweight[2]); } tmpweight = loglkl2weight(a, b, c, i, qweight[0], qweight[1], qweight[2], usebestq_optn); /* tmpweight = loglkl2weight(a, b, c, i, d1, d2, d3, usebestq_optn); */ /* determine best discrete weight */ /* writequartet(a, b, c, i, discreteweight[sqorder[2]]); */ writequartet(a, b, c, i, tmpweight); /* compute sums of topologies per taxon, step by step */ ++(qinfomatr[8][a]); ++(qinfomatr[8][b]); ++(qinfomatr[8][c]); ++(qinfomatr[8][i]); ++(qinfomatr[tmpweight][a]); ++(qinfomatr[tmpweight][b]); ++(qinfomatr[tmpweight][c]); ++(qinfomatr[tmpweight][i]); if ((tmpweight <= 2) || (tmpweight == 4)) { fullresqs++; } else { if (tmpweight == 7) { unresqs++; } else { if (tmpweight == 0) { missingqs++; } else { partresqs++; } } } /* counting completely unresolved quartets */ if (tmpweight == 7) { badqs++; badtaxon[a]++; badtaxon[b]++; badtaxon[c]++; badtaxon[i]++; if (show_optn) { fputid10(unresfp, a); fprintf(unresfp, " "); fputid10(unresfp, b); fprintf(unresfp, " "); fputid10(unresfp, c); fprintf(unresfp, " "); fputid(unresfp, i); fprintf(unresfp, "\n"); } } addtimes(QUARTETS, &tarr); } if (savequartlh_optn) { closefile(lhfp); } if (show_optn) closefile(unresfp); if (mflag == 1) fprintf(STDOUT, "\n"); # endif /* PARALLEL */ } /* computeallquartets */ /* trueID (HAS) */ /* check the branching structure between the leaves (not the taxa!) A, B, C, and I (A, B, C, I don't need to be ordered). As a result, the two leaves that are closer related to each other than to leaf I are found in chooseX and chooseY. If the branching structure is not uniquely defined, chooseX and chooseY are chosen randomly from the possible taxa */ void checkquartet_trueID(int A, /* quartet leaf idx in permutation array */ int B, /* dito. */ int C, /* dito. */ int I, /* dito., to be inserted */ int *trueID, /* permutation array */ int *chooseX, /* (chooseX,chooseY | x,I) */ int *chooseY) /* chooseX+Y are non-neighbors of I */ { int i, j; /* counter */ int a, b; /* temp variable for sorting */ int taxon[5]; /* sorting array for taxa from trueID */ int leaf[5]; /* sorting array for indices in trueID */ int ipos; /* position of leaf I in sorted array */ unsigned char qresult; /* quartet topology */ int notunique = FALSE; /* non-unique topology */ /* The relationship between leaves and taxa is defined by trueID */ taxon[1] = trueID[A]; /* taxon number */ leaf[1] = A; /* leaf index in permutation */ taxon[2] = trueID[B]; leaf[2] = B; taxon[3] = trueID[C]; leaf[3] = C; taxon[4] = trueID[I]; leaf[4] = I; /* sort for taxa */ /* Source: Numerical Recipes (PIKSR2.C) */ for (j = 2; j <= 4; j++) { a = taxon[j]; b = leaf[j]; i = j-1; while (i > 0 && taxon[i] > a) { taxon[i+1] = taxon[i]; leaf[i+1] = leaf[i]; i--; } taxon[i+1] = a; leaf[i+1] = b; } /* where is leaf I ? */ ipos = 1; while (leaf[ipos] != I) ipos++; /* look at sequence quartet */ qresult = readquartet(taxon[1], taxon[2], taxon[3], taxon[4]); /* chooseX and chooseY */ /* qresult is not unique, a covered unique qresult is chosen */ /* and the while loop is circled again (optimizable?) (HAS) */ do { switch (qresult) { /* one single branching structure */ /* 001 */ case 1: if (ipos == 1 || ipos == 2) { *chooseX = leaf[3]; *chooseY = leaf[4]; } else { *chooseX = leaf[1]; *chooseY = leaf[2]; } notunique = FALSE; break; /* 010 */ case 2: if (ipos == 1 || ipos == 3) { *chooseX = leaf[2]; *chooseY = leaf[4]; } else { *chooseX = leaf[1]; *chooseY = leaf[3]; } notunique = FALSE; break; /* 100 */ case 4: if (ipos == 1 || ipos == 4) { *chooseX = leaf[2]; *chooseY = leaf[3]; } else { *chooseX = leaf[1]; *chooseY = leaf[4]; } notunique = FALSE; break; /* two possible branching structures */ /* 011 */ case 3: if (randominteger(2)) qresult = 1; else qresult = 2; notunique = TRUE; break; /* 101 */ case 5: if (randominteger(2)) qresult = 1; else qresult = 4; notunique = TRUE; break; /* 110 */ case 6: if (randominteger(2)) qresult = 2; else qresult = 4; notunique = TRUE; break; /* three possible branching structures */ /* 111 */ case 7: qresult = (1 << randominteger(3)); /* 1, 2, or 4 */ notunique = TRUE; break; /* 000 */ /* empty quartet: missing data -> OK, otherwise ERROR */ case 0: if (readsubset_optn) { *chooseX = -1; *chooseY = -1; } else { # if PARALLEL fprintf(STDOUT, "\n\n\n(%2d)HALT: PLEASE REPORT ERROR K1-PARALLEL TO DEVELOPERS : empty (%d,%d,%d,%d) = %ld\n\n\n", PP_Myid, taxon[1], taxon[2], taxon[3], taxon[4], quart2num(taxon[1], taxon[2], taxon[3], taxon[4])); PP_Finalize(); exit (999); # else fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR K1 TO DEVELOPERS: empty (%d,%d,%d,%d) = %ld\n\n\n", taxon[1], taxon[2], taxon[3], taxon[4], quart2num(taxon[1], taxon[2], taxon[3], taxon[4])); exit (999); # endif } notunique = FALSE; break; default: /* Program error [checkquartet] */ # if PARALLEL fprintf(STDOUT, "\n\n\n(%2d)HALT: PLEASE REPORT ERROR K2-PARALLEL TO DEVELOPERS (%d,%d,%d,%d) = %ld (%d)\n\n\n", PP_Myid, taxon[1], taxon[2], taxon[3], taxon[4], quart2num(taxon[1], taxon[2], taxon[3], taxon[4]), qresult); PP_Finalize(); exit (999); # else fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR K2 TO DEVELOPERS (%d,%d,%d,%d) = %ld (%d)\n\n\n", taxon[1], taxon[2], taxon[3], taxon[4], quart2num(taxon[1], taxon[2], taxon[3], taxon[4]), qresult); exit (999); # endif } /* switch (qresult) */ } while (notunique); return; } /* checkquartet_trueID */ /* un-trueID-ed (HAS) */ /* check the branching structure between the leaves (not the taxa!) A, B, C, and I (A, B, C, I don't need to be ordered). As a result, the two leaves that are closer related to each other than to leaf I are found in chooseX and chooseY. If the branching structure is not uniquely defined, chooseX and chooseY are chosen randomly from the possible taxa */ void checkquartet(int A, /* quartet taxon ID */ int B, /* dito. */ int C, /* dito. */ int I, /* dito., to be inserted */ int *chooseX, /* (chooseX,chooseY | x,I) */ int *chooseY) /* chooseX+Y are non-neighbors of I */ { int i, j; /* counter */ int a; /* temp variable for sorting */ int leaf[5]; /* sorting array */ int ipos; /* position of leaf I in sorted array */ unsigned char qresult; /* quartet topology */ int notunique = FALSE; /* non-unique topology */ /* The relationship between leaves and taxa is defined by trueID */ leaf [1] = A; /* taxon ID of leaf 1 */ leaf [2] = B; /* taxon ID of leaf 2 */ leaf [3] = C; /* taxon ID of leaf 3 */ leaf [4] = I; /* taxon ID of leaf 4 */ /* sort for taxa */ /* Source: Numerical Recipes (PIKSR2.C) */ for (j = 2; j <= 4; j++) { a = leaf[j]; i = j-1; while (i > 0 && leaf[i] > a) { leaf[i+1] = leaf[i]; i--; } leaf[i+1] = a; } /* where is leaf I ? */ ipos = 1; while (leaf[ipos] != I) ipos++; /* look at sequence quartet */ qresult = readquartet(leaf[1], leaf[2], leaf[3], leaf[4]); /* chooseX and chooseY */ /* qresult is not unique, a covered unique qresult is chosen */ /* and the while loop is circled again (optimizable?) (HAS) */ do { switch (qresult) { /* one single branching structure */ /* 001 */ case 1: if (ipos == 1 || ipos == 2) { *chooseX = leaf[3]; *chooseY = leaf[4]; } else { *chooseX = leaf[1]; *chooseY = leaf[2]; } notunique = FALSE; break; /* 010 */ case 2: if (ipos == 1 || ipos == 3) { *chooseX = leaf[2]; *chooseY = leaf[4]; } else { *chooseX = leaf[1]; *chooseY = leaf[3]; } notunique = FALSE; break; /* 100 */ case 4: if (ipos == 1 || ipos == 4) { *chooseX = leaf[2]; *chooseY = leaf[3]; } else { *chooseX = leaf[1]; *chooseY = leaf[4]; } notunique = FALSE; break; /* two possible branching structures */ /* 011 */ case 3: if (randominteger(2)) qresult = 1; else qresult = 2; notunique = TRUE; break; /* 101 */ case 5: if (randominteger(2)) qresult = 1; else qresult = 4; notunique = TRUE; break; /* 110 */ case 6: if (randominteger(2)) qresult = 2; else qresult = 4; notunique = TRUE; break; /* three possible branching structures */ /* 111 */ case 7: qresult = (1 << randominteger(3)); /* 1, 2, or 4 */ notunique = TRUE; break; /* 000 */ /* empty quartet: missing data -> OK, otherwise ERROR */ case 0: if (readsubset_optn) { *chooseX = -1; *chooseY = -1; } else { # if PARALLEL fprintf(STDOUT, "\n\n\n(%2d)HALT: PLEASE REPORT ERROR K1-PARALLEL TO DEVELOPERS : empty (%d,%d,%d,%d) = %ld\n\n\n", PP_Myid, leaf[1], leaf[2], leaf[3], leaf[4], quart2num(leaf[1], leaf[2], leaf[3], leaf[4])); PP_Finalize(); exit (999); # else fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR K1 TO DEVELOPERS: empty (%d,%d,%d,%d) = %ld\n\n\n", leaf[1], leaf[2], leaf[3], leaf[4], quart2num(leaf[1], leaf[2], leaf[3], leaf[4])); exit (999); # endif } notunique = FALSE; break; default: /* Program error [checkquartet] */ # if PARALLEL fprintf(STDOUT, "\n\n\n(%2d)HALT: PLEASE REPORT ERROR K2-PARALLEL TO DEVELOPERS (%d,%d,%d,%d) = %ld (%d)\n\n\n", PP_Myid, leaf[1], leaf[2], leaf[3], leaf[4], quart2num(leaf[1], leaf[2], leaf[3], leaf[4]), qresult); PP_Finalize(); exit (999); # else fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR K2 TO DEVELOPERS (%d,%d,%d,%d) = %ld (%d)\n\n\n", leaf[1], leaf[2], leaf[3], leaf[4], quart2num(leaf[1], leaf[2], leaf[3], leaf[4]), qresult); exit (999); # endif } /* switch (qresult) */ } while (notunique); return; } /* checkquartet */ tree-puzzle-5.2/src/gamma.c0000644000076400001440000002254610073365353011362 /* * gamma.c * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifdef HAVE_CONFIG_H # include #endif #include #include "util.h" #include "gamma.h" /* private prototypes */ static double IncompleteGamma (double x, double alpha, double ln_gamma_alpha); static double PointNormal (double prob); static double PointChi2 (double prob, double v); /* Gamma density function */ double densityGamma (double x, double shape) { return pow (shape, shape) * pow (x, shape-1) / exp (shape*x + LnGamma(shape)); } /* densityGamma */ /* Gamma cdf */ double cdfGamma (double x, double shape) { double result; result = IncompleteGamma (shape*x, shape, LnGamma(shape)); return result; } /* cdfGamma */ /* Gamma inverse cdf */ double icdfGamma (double y, double shape) { double result; result = PointChi2 (y, 2.0*shape)/(2.0*shape); /* to avoid -1.0 */ if (result < 0.0) { result = 0.0; } return result; } /* icdfGamma */ /* Gamma n-th moment */ double momentGamma (int n, double shape) { int i; double tmp = 1.0; for (i = 1; i < n; i++) { tmp *= (shape + i)/shape; } return tmp; } /* momentGamma */ /* The following code comes from tools.c in Yang's PAML package */ double LnGamma (double alpha) { /* returns ln(gamma(alpha)) for alpha>0, accurate to 10 decimal places. Stirling's formula is used for the central polynomial part of the procedure. Pike MC & Hill ID (1966) Algorithm 291: Logarithm of the gamma function. Communications of the Association for Computing Machinery, 9:684 */ double x=alpha, f=0, z; if (x<7) { f=1; z=x-1; while (++z<7) f*=z; x=z; f=-log(f); } z = 1/(x*x); return f + (x-0.5)*log(x) - x + .918938533204673 + (((-.000595238095238*z+.000793650793651)*z-.002777777777778)*z +.083333333333333)/x; } /* LnGamma */ static double IncompleteGamma (double x, double alpha, double ln_gamma_alpha) { /* returns the incomplete gamma ratio I(x,alpha) where x is the upper limit of the integration and alpha is the shape parameter. returns (-1) if in error (1) series expansion if (alpha>x || x<=1) (2) continued fraction otherwise RATNEST FORTRAN by Bhattacharjee GP (1970) The incomplete gamma integral. Applied Statistics, 19: 285-287 (AS32) */ int i; double p=alpha, g=ln_gamma_alpha; double accurate=1e-8, overflow=1e30; double factor, gin=0, rn=0, a=0,b=0,an=0,dif=0, term=0, pn[6]; if (x==0) return (0); if (x<0 || p<=0) return (-1); factor=exp(p*log(x)-x-g); if (x>1 && x>=p) goto l30; /* (1) series expansion */ gin=1; term=1; rn=p; l20: rn++; term*=x/rn; gin+=term; if (term > accurate) goto l20; gin*=factor/p; goto l50; l30: /* (2) continued fraction */ a=1-p; b=a+x+1; term=0; pn[0]=1; pn[1]=x; pn[2]=x+1; pn[3]=x*b; gin=pn[2]/pn[3]; l32: a++; b+=2; term++; an=a*term; for (i=0; i<2; i++) pn[i+4]=b*pn[i+2]-an*pn[i]; if (pn[5] == 0) goto l35; rn=pn[4]/pn[5]; dif=fabs(gin-rn); if (dif>accurate) goto l34; if (dif<=accurate*rn) goto l42; l34: gin=rn; l35: for (i=0; i<4; i++) pn[i]=pn[i+2]; if (fabs(pn[4]) < overflow) goto l32; for (i=0; i<4; i++) pn[i]/=overflow; goto l32; l42: gin=1-factor*gin; l50: return (gin); } /* IncompleteGamma */ /* functions concerning the CDF and percentage points of the gamma and Chi2 distribution */ static double PointNormal (double prob) { /* returns z so that Prob{x.999998 || v<=0) return (-1); g = LnGamma (v/2); xx=v/2; c=xx-1; if (v >= -1.24*log(p)) goto l1; ch=pow((p*xx*exp(g+xx*aa)), 1/xx); if (ch-e<0) return (ch); goto l4; l1: if (v>.32) goto l3; ch=0.4; a=log(1-p); l2: q=ch; p1=1+ch*(4.67+ch); p2=ch*(6.73+ch*(6.66+ch)); t=-0.5+(4.67+2*ch)/p1 - (6.73+ch*(13.32+3*ch))/p2; ch-=(1-exp(a+g+.5*ch+c*aa)*p2/p1)/t; if (fabs(q/ch-1)-.01 <= 0) goto l4; else goto l2; l3: x=PointNormal (p); p1=0.222222/v; ch=v*pow((x*sqrt(p1)+1-p1), 3.0); if (ch>2.2*v+6) ch=-2*(log(1-p)-c*log(.5*ch)+g); l4: do { q=ch; p1=.5*ch; if ((t=IncompleteGamma (p1, xx, g))<0) { return (-1); } p2=p-t; t=p2*exp(xx*aa+g+p1-c*log(ch)); b=t/ch; a=0.5*t-b*c; s1=(210+a*(140+a*(105+a*(84+a*(70+60*a))))) / 420; s2=(420+a*(735+a*(966+a*(1141+1278*a))))/2520; s3=(210+a*(462+a*(707+932*a)))/2520; s4=(252+a*(672+1182*a)+c*(294+a*(889+1740*a)))/5040; s5=(84+264*a+c*(175+606*a))/2520; s6=(120+c*(346+127*c))/5040; ch+=t*(1+0.5*t*s1-b*c*(s1-b*(s2-b*(s3-b*(s4-b*(s5-b*s6)))))); } while (fabs(q/ch-1) > e); return (ch); } /* PointChi2 */ /* Incomplete Gamma function Q(a,x) - this is a cleanroom implementation of NRs gammq(a,x) */ double IncompleteGammaQ (double a, double x) { return 1.0-IncompleteGamma (x, a, LnGamma(a)); } /* IncompleteGammaQ */ /* probability that the observed chi-square exceeds chi2 even if model is correct */ double chi2prob (int deg, double chi2) { return IncompleteGammaQ (0.5*deg, 0.5*chi2); } /* chi2prob */ /* chi square test ef expected frequencies (sum up to 1 !!) of observed frequencies (sum up to the number of samples) numcat number of categories returns critical significance level */ double chi2test(double *ef, int *of, int numcat, int *chi2fail) { double chi2, criticals, efn; int i, below1, below5, reducedcat; int samples; *chi2fail = FALSE; reducedcat = numcat; below1 = 0; below5 = 0; /* compute number of samples */ samples = 0; for (i = 0; i < numcat; i++) { samples = samples + of[i]; # if VERBOSE fprintf(stdout, "of[%d]=%d+ ",i,of[i]); # endif } # if VERBOSE fprintf(stdout, "\nsmp=%d numcat=%d\n",samples, numcat); # endif /* compute chi square */ chi2 = 0; for (i = 0; i < numcat; i++) { efn = ef[i]*((double) samples); if (efn < 1.0) below1++; if (efn < 5.0) below5++; if (efn == 0.0) { reducedcat--; fprintf(stdout, "FPE error: samples=%d, ef[%d]=%e, of[%d]=%d, efn=%e, nc=%d, rc=%d\n", samples, i, ef[i], i, of[i], efn, numcat, reducedcat); fprintf(stdout, "PLEASE REPORT THIS ERROR TO DEVELOPERS !!!\n"); fflush(stdout); } else chi2 = chi2 + ((double) of[i]-efn)*((double) of[i]-efn)/efn; } /* compute significance */ criticals = chi2prob (numcat-1, chi2); /* no expected frequency category (sum up to # samples) below 1.0 */ if (below1 > 0) *chi2fail = TRUE; /* no more than 1/5 of the frequency categories below 5.0 */ if (below5 > (int) floor(samples/5.0)) *chi2fail = TRUE; return criticals; } /* chi2test */ /* chi square test ef expected frequencies (sum up to 1 !!) of observed frequencies (sum up to the number of samples) numcat number of categories returns critical significance level */ double altchi2test(double *ef, int *of, int numcat, int *chi2fail) { double chi2, criticals, efn; int i, below1, below5; int samples; *chi2fail = FALSE; below1 = 0; below5 = 0; /* compute number of samples */ samples = 0; for (i = 0; i < numcat; i++) samples = samples + of[i]; /* compute chi square */ chi2 = 0; for (i = 0; i < numcat; i++) { efn = ef[i]*((double) samples); if (efn < 1.0) below1++; if (efn < 5.0) below5++; chi2 = chi2 + ((double) of[i]-efn)*((double) of[i]-efn)/efn; } /* compute significance */ criticals = chi2prob (numcat-1, chi2); /* no expected frequency category (sum up to # samples) below 1.0 */ if (below1 > 0) *chi2fail = TRUE; /* no more than 1/5 of the frequency categories below 5.0 */ if (below5 > (int) floor(samples/5.0)) *chi2fail = TRUE; return criticals; } /* altchi2test */ tree-puzzle-5.2/src/gamma.h0000644000076400001440000000147610073365360011364 /* * gamma.h * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifndef _GAMMA_ #define _GAMMA_ double densityGamma (double, double); double cdfGamma (double, double); double icdfGamma (double, double); double momentGamma (int, double); double LnGamma (double); double IncompleteGammaQ (double, double); double chi2prob (int, double); double chi2test (double *, int *, int , int *); #endif /* _GAMMA_ */ tree-puzzle-5.2/src/recur-old.c0000644000076400001440000007163510073365364012201 /* * recur-old.c (obsolete) * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ /* initialize tree with the following starting configuration (see pstep.h) */ void inittree_recur(ONEEDGE **edge, /* out: new array of edges */ int **edgeofleaf,/* out: array of external edge ptrs */ int *rootleaf, /* out: rooting leaf (=trueID[0]) */ int Maxspc, /* in: Number of species (n) */ int Maxbrnch, /* in: Number of branches (2n-3) */ int *nextedge, /* out: next free edge index (=3) */ int *nextleaf, /* out: next free leaf index (=3) */ int *trueID) { int i, j; ONEEDGE *tmpedge; int *tmpedgeofleaf; /* allocate the memory for the whole tree */ /* allocate memory for vector with all the edges of the tree */ tmpedge = (ONEEDGE *) calloc((size_t) Maxbrnch, sizeof(ONEEDGE) ); if (tmpedge == NULL) maerror("edge in inittree"); *edge = tmpedge; /* allocate memory for tmpvector with edge numbers of leaves */ tmpedgeofleaf = (int *) calloc((size_t) Maxspc, sizeof(int) ); if (tmpedgeofleaf == NULL) maerror("edgeofleaf in inittree"); for (j = 0; j < Maxspc; j++) tmpedgeofleaf[j]=-1; *edgeofleaf = tmpedgeofleaf; /* allocate memory for all the edges the split map */ for (i = 0; i < Maxbrnch; i++) { (tmpedge)[i].split = (int *) calloc((size_t) Maxspc, sizeof(int) ); (tmpedge)[i].cluster = (int *) calloc((size_t) Maxspc, sizeof(int) ); if (tmpedge[i].cluster == NULL) maerror("edge cluster array in inittree"); (tmpedge)[i].taxon = -1; for (j = 0; j < Maxspc; j++) (tmpedge)[i].cluster[j]=-1; } /* number all edges */ for (i = 0; i < Maxbrnch; i++) tmpedge[i].numedge = i; /* initialize tree */ *nextedge = 3; *nextleaf = 3; #if 0 #endif /* init split vectors: */ /* for edge 0 */ (tmpedge[0].split)[0] = trueID[0]; /* leaf 0 above this edge */ tmpedge[0].upsize = 1; (tmpedge[0].split)[Maxspc-1] = trueID[1]; /* leaf 0 below this edge */ (tmpedge[0].split)[Maxspc-2] = trueID[2]; /* leaf 0 below this edge */ tmpedge[0].downsize = 2; /* for edge 1 */ (tmpedge[1].split)[0] = trueID[0]; /* leaf 0 above this edge */ (tmpedge[1].split)[1] = trueID[2]; /* leaf 0 above this edge */ tmpedge[1].upsize = 2; (tmpedge[1].split)[Maxspc-1] = trueID[1]; /* leaf 0 below this edge */ tmpedge[1].downsize = 1; /* for edge 2 */ (tmpedge[2].split)[0] = trueID[0]; /* leaf 0 above this edge */ (tmpedge[2].split)[1] = trueID[1]; /* leaf 0 above this edge */ tmpedge[2].upsize = 2; (tmpedge[2].split)[Maxspc-1] = trueID[2]; /* leaf 0 below this edge */ tmpedge[2].downsize = 1; #if 0 #endif /* interconnection */ tmpedge[0].up = NULL; tmpedge[0].downleft = &tmpedge[1]; tmpedge[0].downright = &tmpedge[2]; tmpedge[1].up = &tmpedge[0]; tmpedge[1].downleft = NULL; tmpedge[1].downright = NULL; tmpedge[2].up = &tmpedge[0]; tmpedge[2].downleft = NULL; tmpedge[2].downright = NULL; /* taxon IDs of leaves */ tmpedge[0].taxon = trueID[0]; tmpedge[1].taxon = trueID[1]; tmpedge[2].taxon = trueID[2]; /* edges of leaves */ tmpedgeofleaf[trueID[0]] = 0; tmpedgeofleaf[trueID[1]] = 1; tmpedgeofleaf[trueID[2]] = 2; /* uppest edge =: root edge*/ *rootleaf = trueID[0]; } /* inittree_recur */ /******************/ /* free memory (to be called after inittree) */ void freetree_recur(ONEEDGE *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc) /* No. of species */ { int i; /* free split vectors */ for (i = 0; i < 2 * Maxspc - 3; i++) { free(edge[i].split); free(edge[i].cluster); } /* free tree topology */ free(edge); /* free external edge lookup vector */ free(edgeofleaf); } /* freetree_recur */ /******************/ #if 0 /* check edge splits */ void check_recur( ONEEDGE *edge, /* edge array */ int Maxspc, /* No. of species */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *permut) { int n,m; fprintf(stderr, "Permutation: "); for (m = 0; m %d != %d>\n", m, (edge[m].taxon >= 0) ? 'e' : 'i', edge[m].taxon, edge[m].upsize, edge[m].downsize, edge[m].upsize+edge[m].downsize, nextleaf); fprintf(stderr, " UP:"); for (n = 0; n %d == %d> OK\n", m, (edge[m].taxon >= 0) ? 'e' : 'i', edge[m].taxon, edge[m].upsize, edge[m].downsize, edge[m].upsize+edge[m].downsize, nextleaf); } } } void updatesplit_split(ONEEDGE *curredge, /* current edge */ int wherefrom, /* direction to last curr. edge */ int newleaf, /* leaf to add to splits */ ONEEDGE *edge, /* edge array */ int Maxspc, /* No. of species */ int Maxbrnch, /* No. of branches */ int *edgeofleaf, /* ext. edge idx array */ int in_nextedge, /* next free edge idx */ int in_nextleaf) /* next free leaf idx */ { switch (wherefrom) { case UP: fprintf(stderr, "UUU: updating edge %d (from UP) split[%d]:=%d\n", curredge->numedge, curredge->upsize, newleaf); curredge->split[(curredge->upsize)++] = newleaf; /* leaf is up */ if (curredge->downright != NULL) { /* not leaf */ updatesplit_split(curredge->downright, UP, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); updatesplit_split(curredge->downleft, UP, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } else { /* nothing to do */ return; } break; case DOWNLEFT: fprintf(stderr, "UUU: updating edge %d (from DOWNLEFT) split[%d]:=%d\n", curredge->numedge, Maxspc - (curredge->downsize) +1, newleaf); curredge->split[Maxspc - ++(curredge->downsize)] = newleaf; /* leaf is down */ if (curredge->downright != NULL) { /* not leaf */ updatesplit_split(curredge->downright, UP, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } if (curredge->up != NULL) { /* not root */ if ((curredge->up)->downright == curredge) { updatesplit_split(curredge->up, DOWNRIGHT, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } else { updatesplit_split(curredge->up, DOWNLEFT, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } } break; case DOWNRIGHT: fprintf(stderr, "UUU: updating edge %d (from DOWNRIGHT) split[%d]:=%d\n", curredge->numedge, Maxspc - (curredge->downsize) +1, newleaf); curredge->split[Maxspc - ++(curredge->downsize)] = newleaf; /* leaf is down */ if (curredge->downright != NULL) { /* not leaf */ updatesplit_split(curredge->downleft, UP, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } if ((curredge->up) != NULL) { /* not root */ if ((curredge->up)->downright == curredge) { updatesplit_split(curredge->up, DOWNRIGHT, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } else { updatesplit_split(curredge->up, DOWNLEFT, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } } break; } } /* updatesplit_split */ /******************/ /* add next leaf on the specified edge */ void updatetreesplits_split(int dockedge, /* dockedge */ int newleaf, /* leaf to add to splits */ ONEEDGE *edge, /* edge array */ int Maxspc, /* No. of species */ int *edgeofleaf, /* ext. edge idx array */ int in_nextedge, /* next free edge idx */ int in_nextleaf, /* next free leaf idx */ ivector permut) { int n; /* counter */ int wherefrom; /* direction to last edge */ ONEEDGE *curredge; /* edge array */ /* copy clusters from dockedge to in_nextedge */ /* up-cluster: upsize-1 .. 0 */ for (n=(edge[dockedge].upsize) - 1; n >= 0; n--) { (edge[in_nextedge]).split[n] = (edge[dockedge]).split[n]; } (edge[in_nextedge]).upsize = (edge[dockedge]).upsize; /* down-cluster: downsize .. Maxspc-1 */ for (n=Maxspc - (edge[dockedge]).downsize; n < Maxspc; n++) { (edge[in_nextedge]).split[n] = (edge[dockedge]).split[n]; } (edge[in_nextedge]).downsize = (edge[dockedge]).downsize; /* add the new taxon to in_nextedge */ (edge[in_nextedge]).split[Maxspc - ++((edge[in_nextedge]).downsize)] = permut[in_nextleaf]; /* setup clusters for new external edge (in_nextedge+1) */ /* up-cluster: all taxa in tree */ for (n=0; n < in_nextleaf; n++) { (edge[in_nextedge+1]).split[n] = permut[n]; } (edge[in_nextedge+1]).upsize = in_nextleaf; /* down-cluster: the new taxon itself */ (edge[in_nextedge+1]).split[Maxspc-1] = permut[in_nextleaf]; (edge[in_nextedge+1]).downsize = 1; curredge = &(edge[in_nextedge]); if (curredge->up != NULL) { /* not root */ if (((curredge->up)->downright) == curredge) { wherefrom = DOWNRIGHT; } else { wherefrom = DOWNLEFT; } /* climbing up from insertion point */ updatesplit_split(curredge->up, wherefrom, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } /* climbing down to dockedge from insertion point */ updatesplit_split(&(edge[dockedge]), UP, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } /* updatetreesplits_split */ #endif /******************/ /* add next leaf on the specified edge */ void addnextleaf_recur(int dockedge, /* insert here */ ONEEDGE *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int rootleaf, /* uppest leaf */ int Maxspc, /* No. of species */ int Maxbrnch, /* No. of branches */ int *in_nextedge, /* next free edge idx */ int *in_nextleaf, /* next free leaf idx */ ivector permut) { int nextedge; int nextleaf; nextedge=*in_nextedge; nextleaf=*in_nextleaf; if (dockedge >= nextedge) { fprintf(stderr, "de=%d ne=%d\n", dockedge, nextedge); /* Trying to add leaf nextleaf to nonexisting edge dockedge */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR F TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } if (nextleaf >= Maxspc) { /* Trying to add leaf nextleaf to a tree with Maxspc leaves */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR G TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } /* necessary change in edgeofleaf if dockedge == root edge */ if (edgeofleaf[rootleaf] == dockedge) edgeofleaf[rootleaf] = nextedge; /* adding nextedge to the tree */ edge[nextedge].up = edge[dockedge].up; edge[nextedge].downleft = &edge[dockedge]; edge[nextedge].downright = &edge[nextedge+1]; edge[dockedge].up = &edge[nextedge]; /* if not root edge: connect ancestor to internal edge (nextedge) */ if (edge[nextedge].up != NULL) { if ( ((edge[nextedge].up)->downleft) == &edge[dockedge] ) (edge[nextedge].up)->downleft = &edge[nextedge]; else (edge[nextedge].up)->downright = &edge[nextedge]; } /* adding new external edge (nextedge+1) to the tree */ edge[nextedge+1].up = &edge[nextedge]; edge[nextedge+1].downleft = NULL; edge[nextedge+1].downright = NULL; edge[nextedge+1].taxon = permut[nextleaf]; edgeofleaf[permut[nextleaf]] = nextedge+1; #if 0 updatetreesplits_split(dockedge, permut[nextleaf], edge, Maxspc, edgeofleaf, nextedge, nextleaf, permut); #endif (*in_nextedge) += 2; (*in_nextleaf) ++; } /* addnextleaf_recur */ /******************/ /* compute edge penalties using splits, if #minedges>1 choose one randomly */ void computepenalties_recur(ONEEDGE *curredge, /* edge array */ int Maxspc, /* number of taxa */ ulimatrix neighbormatr, /* neighborhood matrix */ ulivector leafpenalty, /* leaf edge penalties */ int *minedges, /* minimum edge vector */ int *howmany, /* number minimum edge */ uli *minpenalty) /* minimum penalty */ { int l, r; int lmax, rmax; int taxon; int size; int rID; uli temp; ONEEDGE *left; /* temp edge ptr */ ONEEDGE *right; /* temp edge ptr */ if (curredge->downleft == NULL) { /* leaf edge */ taxon = curredge->taxon; curredge->cluster[0] = taxon; curredge->clsize = 1; curredge->edgeinfo = leafpenalty[taxon]; curredge->allsum = leafpenalty[taxon]; curredge->submatrsum = 0; if (*minpenalty == curredge->edgeinfo) { /* another min edge */ minedges[(*howmany)++] = curredge->numedge; } else { /* -> not same minimum */ if (*minpenalty > curredge->edgeinfo) { /* new minimum penalty */ *howmany = 1; minedges[0] = curredge->numedge; *minpenalty = curredge->edgeinfo; } /* if new minimum */ } /* same minimum */ } else { /* -> internal edge */ left = curredge->downleft; right = curredge->downright; /* descend downleft */ computepenalties_recur(left, Maxspc, neighbormatr, leafpenalty, minedges, howmany, minpenalty); /* descend downright */ computepenalties_recur(right, Maxspc, neighbormatr, leafpenalty, minedges, howmany, minpenalty); lmax = left->clsize; for (l= 0; lcluster[l] = left->cluster[l]; } size = lmax; rmax = right->clsize; temp = 0; for (r= 0; rcluster[r]; /* copy right cluster */ curredge->cluster[size++] = rID; /* sum up sub neighborhood matrix */ for (l= 0; lcluster[l]][rID]; } } curredge->clsize = size; /* compute edge penalty */ curredge->submatrsum = 2*temp + left->submatrsum + right->submatrsum; curredge->allsum = left->allsum + right->allsum; curredge->edgeinfo = curredge->allsum - curredge->submatrsum; if (*minpenalty == curredge->edgeinfo) { /* another min edge */ minedges[(*howmany)++] = curredge->numedge; } else { /* -> not same minimum */ if (*minpenalty > curredge->edgeinfo) { /* new minimum penalty */ *howmany = 1; minedges[0] = curredge->numedge; *minpenalty = curredge->edgeinfo; } /* if new minimum */ } /* same minimum */ ; } fprintf(stderr, "PPP e[%2d]%c t(%2d) %2ld <--> %2ld new penalty\n", curredge->numedge, (curredge->taxon >= 0) ? 'e' : 'i', curredge->taxon, curredge->penalty, curredge->edgeinfo); } /* computepenalties_recur */ /******************/ /* compute edge penalties using splits, if #minedges>1 choose one randomly */ void computepenaltiestree_recur(ONEEDGE *tmpedge, /* edge array */ int *edgeofleaf, /* external edge ptrs */ int rootleaf, /* idx of uppest edge */ int nextleaf, /* next free leaf idx */ int Maxspc, /* number of taxa */ ulimatrix neighbormatr, /* neighborhood matrix */ ulivector leafpenalty, /* leaf edge penalties */ int **out_minedges, /* minimum edge vector */ int *out_howmany, /* number minimum edge */ uli *out_minpenalty, /* minimum penalty */ int *out_minedge) /* minimum edge */ { int rootedge; int lmax, rmax; int l, r; int howmany = 0; int *minedges = *out_minedges; uli temp; ONEEDGE *left; /* temp edge ptr */ ONEEDGE *right; /* temp edge ptr */ uli minpenalty; uli submatrsum; uli allsum; uli edgeinfo; ONEEDGE *curredge; rootedge = edgeofleaf[rootleaf]; curredge = &(tmpedge[rootedge]); curredge->edgeinfo = leafpenalty[rootleaf]; fprintf(stderr, "PPP e[%2d]%c t(%2d) %2ld <--> %2ld new penalty\n", curredge->numedge, (curredge->taxon >= 0) ? 'e' : 'i', curredge->taxon, curredge->penalty, curredge->edgeinfo); if (minedges == NULL) minedges = (int *) calloc((size_t) Maxspc, sizeof(int)); /* first edge: init */ minedges[0] = rootedge; howmany = 1; minpenalty = curredge->edgeinfo; left = curredge->downleft; right = curredge->downright; /* descend downleft */ computepenalties_recur(left, Maxspc, neighbormatr, leafpenalty, minedges, &howmany, &minpenalty); /* descend downright */ computepenalties_recur(right, Maxspc, neighbormatr, leafpenalty, minedges, &howmany, &minpenalty); lmax = left->clsize; rmax = right->clsize; if ((lmax + rmax) != (nextleaf-1)) { /* root edge cluster should yield all other leaves */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR HSCL1 TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } temp = 0; for (r= 0; rcluster[l]][right->cluster[r]]; } } /* compute edge penalty */ submatrsum = 2*temp + left->submatrsum + right->submatrsum; allsum = left->allsum + right->allsum; edgeinfo = allsum - submatrsum; if ((edgeinfo) != (curredge->edgeinfo)) fprintf(stderr, "%ld != %ld\n", edgeinfo, curredge->edgeinfo); else fprintf(stderr, "%ld == %ld\n", edgeinfo, curredge->edgeinfo); if ((edgeinfo) != (curredge->edgeinfo)) { /* root edge cluster should yield all other leaves */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR HSCL2 TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } if (howmany > 1) { /* draw random edge */ int i, k, randomnum; randomnum = randominteger(howmany) + 1; /* 1 to howmany */ i = -1; for (k = 0; k < randomnum; k++) { do { i++; } while (tmpedge[i].edgeinfo != minpenalty); *out_minedge = tmpedge[i].numedge; } } else { *out_minedge = minedges[0]; } #if 0 /* optimization (HAS) */ if (howmany > 1) *out_minedge = minedges[randominteger(howmany)]; else *out_minedge = minedges[0]; #endif *out_howmany = howmany; *out_minpenalty = minpenalty; } /* computepenaltiestree_recur */ /******************/ #if 0 /* compute edge penalties using splits, if #minedges>1 choose one randomly */ void computepenalties_split(ONEEDGE *tmpedge, /* edge array */ int nextedge, /* next free edge idx */ int Maxspc, /* number of taxa */ ulimatrix neighbormatr, /* neighborhood matrix */ int **out_minedges, /* minimum edge vector */ int *out_howmany, /* number minimum edge */ uli *out_minpenalty, /* minimum penalty */ int *out_minedge) /* minimum edge */ { int i; /* counter */ int a, b; int idxA, idxB; int maxUP; /* index counter for right/left split cluster */ int howmany = 0; int *minedges = *out_minedges; uli minpenalty; for (i = 0; i < nextedge; i++) { (tmpedge[i]).penalty = 0; /* reset penalty */ maxUP = (tmpedge[i]).upsize; #if 0 fprintf(stderr, "<%d>", i); for (idxA = 0; idxA < maxUP; idxA++) fprintf(stderr, "%d,", (tmpedge[i].split)[idxA]); fprintf(stderr, "(%d) || ", (tmpedge[i]).upsize); for (idxB = Maxspc - (tmpedge[i]).downsize; idxB < Maxspc; idxB++) fprintf(stderr, "%d,", (tmpedge[i].split)[idxB]); fprintf(stderr, "(%d)\n", (tmpedge[i]).downsize); #endif for (idxB = Maxspc - (tmpedge[i]).downsize; idxB < Maxspc; idxB++) { b = (tmpedge[i].split)[idxB]; for (idxA = 0; idxA < maxUP; idxA++) { a = (tmpedge[i].split)[idxA]; (tmpedge[i]).penalty += neighbormatr[a][b]; #if 0 fprintf(stderr, "<%d> %d(%d)->%d(%d) : %ld ---> p[%d]=%ld\n", i, a, idxA, b, idxB, neighbormatr[a][b], i, (tmpedge[i]).penalty); #endif } /* for all root-sided (up) taxa */ } /* for all non-root-sided (down) taxa */ if (howmany == 0) { /* first edge: init */ if (minedges == NULL) minedges = (int *) calloc((size_t) Maxspc, sizeof(int)); minedges[howmany++] = i; minpenalty = tmpedge[i].penalty; } else { /* -> all other edges */ if (minpenalty == tmpedge[i].penalty) { /* another min edge */ minedges[howmany++] = i; } else { /* -> not same minimum */ if (minpenalty > tmpedge[i].penalty) { /* new minimum penalty */ howmany = 0; minedges[howmany++] = i; minpenalty = tmpedge[i].penalty; } /* if new minimum */ } /* same minimum */ } /* if all other edges */ } /* for all edges */ *out_howmany = howmany, *out_minpenalty = minpenalty; #if 0 if (howmany > 1) *out_minedge = minedges[0]; else *out_minedge = minedges[0]; #endif } /* computepenalties_split */ #endif /******************/ /* trueID-ed (HAS) */ /* perform one single puzzling step to produce one intermediate tree */ void onepstep_recur( /* PStep (intermediate) tree topol: */ ONEEDGE **edge, /* out: new array of edges */ int **edgeofleaf, /* out: array of extern edge ptrs */ int *rootleaf, /* out: root leaf in topol, starting perm[0] */ unsigned char *quartettopols, /* in: quartetblock with all topols */ int Maxspc, /* in: Number of species (n) */ ivector permut) /* in: species permutation (trueID) */ { /* local variables: */ int Maxbrnch = (2*Maxspc)-3; /* Number of branches (2n-3) */ int nextedge; /* next free edge index (=3) */ int nextleaf; /* next free leaf index (=3) */ int minedge; /* insertion edge of minimum penalty */ uli mininfo; /* minimum penalty */ int a, b, c, i; /* quartet leaves, i to be inserted */ int idxA, idxB; int idxC, idxI; /* index counter for quartet leaves */ int chooseX, chooseY; /* end leaves of penalty path */ ONEEDGE *tmpedge; /* new array of edges */ int *tmpedgeofleaf; /* array of extern edge ptrs */ int tmprootleaf; /* root edge */ ulimatrix neighbormatr; ulivector leafpenalty; int *minedges = NULL; int howmany; neighbormatr = new_ulimatrix(Maxspc,Maxspc); leafpenalty = new_ulivector(Maxspc); /* allocate and initialize new tree topology */ inittree_recur(&tmpedge, &tmpedgeofleaf, &tmprootleaf, Maxspc, Maxbrnch, &nextedge, &nextleaf, permut); /* check_recur(tmpedge, Maxspc, tmpedgeofleaf, nextedge, nextleaf, permut); */ fprintf(stderr, "----------------------------------------------\n"); for (idxI = 3; idxI < Maxspc; idxI++) { i = permut[idxI]; /* clear all edgeinfos */ /* resetedgeinfo(tmpedge, nextedge); */ /* initialize penalty neighborhood matrix */ for (idxA = 0; idxA < Maxspc; idxA++) { a = permut[idxA]; for (idxB = 0; idxB < Maxspc; idxB++) { b = permut[idxB]; if (a != b) { neighbormatr[a][b] = -1; neighbormatr[b][a] = -1; } else { neighbormatr[a][b] = 0; neighbormatr[b][a] = 0; } } } /* for all entries in the upper neighbormatr */ /* initialize penalty neighborhood matrix + leafpenalty vector */ for (idxA = 0; idxA < nextleaf - 1; idxA++) { a = permut[idxA]; leafpenalty[a] = 0; for (idxB = idxA + 1; idxB < nextleaf; idxB++) { b = permut[idxB]; neighbormatr[a][b] = 0; neighbormatr[b][a] = 0; } } /* for all entries in the upper neighbormatr */ /* * core of quartet puzzling algorithm */ for (idxA = 0; idxA < nextleaf - 2; idxA++) { a = permut[idxA]; for (idxB = idxA + 1; idxB < nextleaf - 1; idxB++) { b = permut[idxB]; for (idxC = idxB + 1; idxC < nextleaf; idxC++) { c = permut[idxC]; /* check which two leaves out of a,b,c are closer related to each other than to leaf i according to a least squares fit of the continous Bayesian weights to the seven trivial "attractive regions". We assign a score of 1 to all edges on the penalty path between these two leaves chooseX and chooseY */ /* de-trueID-ed (HAS) */ checkquartet(a, b, c, i, &chooseX, &chooseY); (neighbormatr[chooseX][chooseY])++; } /* for all quartets q=(a,b,c,i): c */ } /* for all quartets q=(a,b,c,i): b */ } /* for all quartets q=(a,b,c,i): a */ /* symetrize penalty neighborhood matrix */ for (idxA = 0; idxA < nextleaf - 1; idxA++) { a = permut[idxA]; for (idxB = idxA + 1; idxB < nextleaf; idxB++) { b = permut[idxB]; neighbormatr[a][b] += neighbormatr[b][a]; neighbormatr[b][a] = neighbormatr[a][b]; leafpenalty[a] += neighbormatr[a][b]; leafpenalty[b] += neighbormatr[a][b]; } } /* for all entries in the upper neighbormatr */ for (idxA = 0; idxA < Maxspc; idxA++) fprintf(stderr, "%4d", idxA); fprintf(stderr, " perm\n"); for (idxA = 0; idxA < Maxspc; idxA++) fprintf(stderr, "%4d", permut[idxA]); fprintf(stderr, " %d taxa\n\n", nextleaf); for (idxA = 0; idxA < Maxspc; idxA++) { a = permut[idxA]; for (idxB = 0; idxB < Maxspc; idxB++) { b = permut[idxB]; fprintf(stderr, "%4ld", neighbormatr[a][b]); } fprintf(stderr, "\n"); } fprintf(stderr, "\n"); for (idxA = 0; idxA < Maxspc; idxA++) { a = permut[idxA]; fprintf(stderr, "%4ld", leafpenalty[a]); } fprintf(stderr, "\n"); #if 0 computepenalties_split(tmpedge, nextedge, Maxspc, neighbormatr, &minedges, &howmany, &mininfo, &minedge); #endif computepenaltiestree_recur(tmpedge, tmpedgeofleaf, tmprootleaf, nextleaf, Maxspc, neighbormatr, leafpenalty, &minedges, &howmany, &mininfo, &minedge); {int n; for(n=0; n= 0) ? 'e' : 'i', tmpedge[n].taxon, tmpedge[n].penalty, tmpedge[n].edgeinfo); } else { fprintf(stderr, "PPP e[%2d]%c t(%2d) %2ld != %2ld new ERROR\n", n, (tmpedge[n].taxon >= 0) ? 'e' : 'i', tmpedge[n].taxon, tmpedge[n].penalty, tmpedge[n].edgeinfo); } } } /* add the next leaf on minedge */ addnextleaf_recur(minedge, tmpedge, tmpedgeofleaf, tmprootleaf, Maxspc, Maxbrnch, &nextedge, &nextleaf, permut); fprintf(stderr, "----------------------------------------------\n"); } /* adding all other leafs */ *edge = tmpedge; /* export tree topology */ *edgeofleaf = tmpedgeofleaf; /* export array of extern edge ptrs */ *rootleaf = tmprootleaf; /* export root edge */ } /* onepstep_recur */ tree-puzzle-5.2/src/Makefile.am0000644000076400001440000002206310073365370012161 # # Makefile.am # # # Part of TREE-PUZZLE 5.2 (July 2004) # # (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler # (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, # M. Vingron, and Arndt von Haeseler # (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler # # All parts of the source except where indicated are distributed under # the GNU public licence. See http://www.opensource.org for details. # # ($Id$) # SUBDIRS = sprng bin_PROGRAMS = puzzle @PPUZZLE@ EXTRA_PROGRAMS = ppuzzle EXTRA_DIST = \ pstep-deglob.c\ pstep-deglob.h\ pstep-mrca.c\ pstep-mrca.h\ pstep-orig.c\ pstep-orig.h\ pstep-recursive.c\ pstep-recursive.h\ split.c \ recur.c \ recur-old.c \ mrca.c \ pstep-split.c\ pstep-split.h\ subsetmatr.c\ subsetmatr.h\ pstep-trueID.c\ pstep-trueID.h SPRNG_OBJ = makeseed.$(OBJEXT) store.$(OBJEXT) memory.$(OBJEXT) checkid.$(OBJEXT) lcg64.$(OBJEXT) primes-lcg64.$(OBJEXT) SPRNG_DIR_OBJ = sprng/makeseed.$(OBJEXT) sprng/store.$(OBJEXT) sprng/memory.$(OBJEXT) sprng/checkid.$(OBJEXT) sprng/lcg64.$(OBJEXT) sprng/primes-lcg64.$(OBJEXT) #SPRNG_OBJ = sprng/makeseed.$(OBJEXT) sprng/store.$(OBJEXT) sprng/memory.$(OBJEXT) sprng/checkid.$(OBJEXT) sprng/lcg64.$(OBJEXT) sprng/primes-lcg64.$(OBJEXT) #SPRNG_LFG_SRCS = sprng/lfg.c sprng/interface.h sprng/makeseed.c sprng/memory.c sprng/checkid.c sprng/store.c #SPRNG_LFG_OBJS = sprng/lfg.$(OBJEXT) sprng/makeseed.$(OBJEXT) sprng/memory.$(OBJEXT) sprng/checkid.$(OBJEXT) sprng/store.$(OBJEXT) #SPRNG_MLFG_SRCS = sprng/mlfg.c sprng/interface.h sprng/makeseed.c sprng/memory.c sprng/checkid.c sprng/store.c sprng/int64.h #SPRNG_MLFG_OBJS = sprng/mlfg.$(OBJEXT) sprng/makeseed.$(OBJEXT) sprng/memory.$(OBJEXT) sprng/checkid.$(OBJEXT) sprng/store.$(OBJEXT) #SPRNG_LCG_SRCS = sprng/lcg.c sprng/interface.h sprng/primes-lcg.c sprng/makeseed.c sprng/memory.c sprng/checkid.c sprng/store.c #SPRNG_LCG_OBJS = sprng/lcg.$(OBJEXT) sprng/primes-lcg.$(OBJEXT) sprng/makeseed.$(OBJEXT) sprng/memory.$(OBJEXT) sprng/checkid.$(OBJEXT) sprng/store.$(OBJEXT) #SPRNG_CMRG_SRCS = sprng/lcg64.c sprng/interface.h sprng/primes-lcg64.c sprng/makeseed.c sprng/memory.c sprng/checkid.c sprng/store.c #SPRNG_CMRG_OBJS = sprng/lcg64.$(OBJEXT) sprng/primes-lcg64.$(OBJEXT) sprng/makeseed.$(OBJEXT) sprng/memory.$(OBJEXT) sprng/checkid.$(OBJEXT) sprng/store.$(OBJEXT) #SPRNG_LCG64_SRCS = sprng/lcg64.c sprng/interface.h sprng/primes-lcg64.c sprng/makeseed.c sprng/memory.c sprng/checkid.c sprng/store.c #SPRNG_LCG64_OBJS = sprng/lcg64.$(OBJEXT) sprng/primes-lcg64.$(OBJEXT) sprng/makeseed.$(OBJEXT) sprng/memory.$(OBJEXT) sprng/checkid.$(OBJEXT) sprng/store.$(OBJEXT) puzzle_SOURCES = gamma.c ml1.c ml2.c mlparam.c model1.c model2.c puzzle1.c puzzle2.c pstep.c util.c consensus.c treesort.c treetest.c ml.h util.h puzzle.h pstep.h gamma.h consensus.h treesort.h treetest.h #puzzle_LDADD = sgamma.o sml1.o sml2.o smlparam.o smodel1.o smodel2.o spuzzle1.o spuzzle2.o spstep.o sutil.o sconsensus.o streesort.o sprng/liblcg64.a puzzle_LDADD = sgamma.$(OBJEXT) sml1.$(OBJEXT) sml2.$(OBJEXT) smlparam.$(OBJEXT) smodel1.$(OBJEXT) smodel2.$(OBJEXT) spuzzle1.$(OBJEXT) spuzzle2.$(OBJEXT) spstep.$(OBJEXT) sutil.$(OBJEXT) sconsensus.$(OBJEXT) streesort.$(OBJEXT) streetest.$(OBJEXT) INCLUDES = -I. -I.. -I$(srcdir) -I$(srcdir)/sprng SDEFS = SCFLAGS = SLDFLAGS = SLDLIBS = @LIBS@ SCOMPILE = $(CC) $(SDEFS) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(SCFLAGS) $(CFLAGS) SCCLD = $(CC) SLINK = $(SCCLD) $(AM_CFLAGS) $(CFLAGS) $(SLDFLAGS) $(LDFLAGS) ppuzzle_SOURCES = gamma.c ml1.c ml2.c mlparam.c model1.c model2.c puzzle1.c puzzle2.c pstep.c sched.c util.c consensus.c treesort.c treetest.c ppuzzle.c ml.h util.h puzzle.h pstep.h gamma.h ppuzzle.h sched.h consensus.h treesort.h treetest.h ppuzzle_LDADD = pgamma.$(OBJEXT) pml1.$(OBJEXT) pml2.$(OBJEXT) pmlparam.$(OBJEXT) pmodel1.$(OBJEXT) pmodel2.$(OBJEXT) ppuzzle1.$(OBJEXT) ppuzzle2.$(OBJEXT) ppstep.$(OBJEXT) psched.$(OBJEXT) putil.$(OBJEXT) pconsensus.$(OBJEXT) ptreesort.$(OBJEXT) ptreetest.$(OBJEXT) ppuzzle.$(OBJEXT) PCC = @MPICC@ PDEFS = -DPARALLEL PCFLAGS = PLDFLAGS = PLDLIBS = @LIBS@ @MPILIBS@ PCOMPILE = $(PCC) $(PDEFS) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(PCFLAGS) $(CFLAGS) PCCLD = $(PCC) PLINK = $(PCCLD) $(AM_CFLAGS) $(PCFLAGS) $(CFLAGS) $(PLDFLAGS) $(LDFLAGS) make-sprng-objs: cd sprng && $(MAKE) $(SPRNG_OBJ) puzzle$(EXEEXT): $(puzzle_LDADD) $(puzzle_SOURCES) make-sprng-objs Makefile $(SLINK) $(puzzle_LDADD) $(SPRNG_DIR_OBJ) $(SLDLIBS) -o $@ sml1.$(OBJEXT): ml1.c ml.h util.h Makefile $(SCOMPILE) -c $(srcdir)/ml1.c && mv ml1.$(OBJEXT) $@ sml2.$(OBJEXT): ml2.c ml.h util.h Makefile $(SCOMPILE) -c $(srcdir)/ml2.c && mv ml2.$(OBJEXT) $@ smlparam.$(OBJEXT): mlparam.c ml.h util.h gamma.h Makefile $(SCOMPILE) -c $(srcdir)/mlparam.c && mv mlparam.$(OBJEXT) $@ smodel1.$(OBJEXT): model1.c ml.h util.h Makefile $(SCOMPILE) -c $(srcdir)/model1.c && mv model1.$(OBJEXT) $@ smodel2.$(OBJEXT): model2.c ml.h util.h Makefile $(SCOMPILE) -c $(srcdir)/model2.c && mv model2.$(OBJEXT) $@ spuzzle1.$(OBJEXT): puzzle1.c ml.h util.h puzzle.h gamma.h ppuzzle.h Makefile $(SCOMPILE) -c $(srcdir)/puzzle1.c && mv puzzle1.$(OBJEXT) $@ spuzzle2.$(OBJEXT): puzzle2.c ml.h util.h puzzle.h ppuzzle.h Makefile $(SCOMPILE) -c $(srcdir)/puzzle2.c && mv puzzle2.$(OBJEXT) $@ spstep.$(OBJEXT): pstep.c ml.h util.h puzzle.h ppuzzle.h Makefile $(SCOMPILE) -c $(srcdir)/pstep.c && mv pstep.$(OBJEXT) $@ sutil.$(OBJEXT): util.c util.h Makefile $(SCOMPILE) -c $(srcdir)/util.c && mv util.$(OBJEXT) $@ sgamma.$(OBJEXT): gamma.c gamma.h util.h Makefile $(SCOMPILE) -c $(srcdir)/gamma.c && mv gamma.$(OBJEXT) $@ sconsensus.$(OBJEXT): consensus.c consensus.h util.h Makefile $(SCOMPILE) -c $(srcdir)/consensus.c && mv consensus.$(OBJEXT) $@ streesort.$(OBJEXT): treesort.c treesort.h util.h Makefile $(SCOMPILE) -c $(srcdir)/treesort.c && mv treesort.$(OBJEXT) $@ streetest.$(OBJEXT): treetest.c treetest.h util.h Makefile $(SCOMPILE) -c $(srcdir)/treetest.c && mv treetest.$(OBJEXT) $@ # #SPRNG # ## sprng/makeseed.$(OBJEXT) : sprng/makeseed.c ## $(CC) -c $(CFLAGS) sprng/makeseed.c ## ## sprng/store.$(OBJEXT) : sprng/store.c sprng/store.h ## $(CC) -c $(CFLAGS) sprng/store.c ## ## sprng/memory.$(OBJEXT) : sprng/memory.c ## $(CC) -c $(CFLAGS) sprng/memory.c ## ## sprng/checkid.$(OBJEXT) : sprng/checkid.c sprng/memory.h ## $(CC) -c $(CFLAGS) sprng/checkid.c ## ## sprng/lcg64.$(OBJEXT) : sprng/interface.h sprng/lcg64.c sprng/memory.h sprng/primes.h sprng/multiply.h sprng/store.h ## $(CC) -c $(CFLAGS) $(FFXN) $(INLINEOPT) lcg64.c ## ## sprng/primes-lcg64.$(OBJEXT) : sprng/primes-lcg64.h sprng/primes-lcg64.c sprng/primelist-lcg64.h ## $(CC) -c $(CFLAGS) primes-lcg64.c ## ## #sprng/lcg64.a: ## # $(CD) sprng; $(make) ## ## #sprng.h: ## # $(CP) $(srcdir)/sprng-1.0/include/sprng.h $@ ## #interface.h: ## # $(CP) $(srcdir)/sprng-1.0/include/interface.h $@ ## #slcg64.o : interface.h lcg64.c memory.h primes.h multiply.h store.h ## # $(SCOMPILE) -c $(srcdir)/lcg64.c && mv lcg64.o $@ ## #plcg64.o : interface.h lcg64.c memory.h primes.h multiply.h store.h ## # $(SCOMPILE) -c $(srcdir)/lcg64.c && mv lcg64.o $@ ## # ## #primes.o : primes.h primes.c ## # $(CC) -c $(CFLAGS) primes.c -I$(SRCDIR) ppuzzle$(EXEEXT): $(ppuzzle_LDADD) $(ppuzzle_SOURCES) make-sprng-objs Makefile $(PLINK) $(ppuzzle_LDADD) $(SPRNG_DIR_OBJ) $(PLDLIBS) -o $@ pml1.$(OBJEXT): ml1.c ml.h util.h Makefile $(PCOMPILE) -c $(srcdir)/ml1.c && mv ml1.$(OBJEXT) $@ pml2.$(OBJEXT): ml2.c ml.h util.h Makefile $(PCOMPILE) -c $(srcdir)/ml2.c && mv ml2.$(OBJEXT) $@ pmlparam.$(OBJEXT): mlparam.c ml.h util.h gamma.h Makefile $(PCOMPILE) -c $(srcdir)/mlparam.c && mv mlparam.$(OBJEXT) $@ pmodel1.$(OBJEXT): model1.c ml.h util.h Makefile $(PCOMPILE) -c $(srcdir)/model1.c && mv model1.$(OBJEXT) $@ pmodel2.$(OBJEXT): model2.c ml.h util.h Makefile $(PCOMPILE) -c $(srcdir)/model2.c && mv model2.$(OBJEXT) $@ ppuzzle1.$(OBJEXT): puzzle1.c ml.h util.h puzzle.h gamma.h ppuzzle.h Makefile $(PCOMPILE) -c $(srcdir)/puzzle1.c && mv puzzle1.$(OBJEXT) $@ ppuzzle2.$(OBJEXT): puzzle2.c ml.h util.h puzzle.h ppuzzle.h Makefile $(PCOMPILE) -c $(srcdir)/puzzle2.c && mv puzzle2.$(OBJEXT) $@ ppstep.$(OBJEXT): pstep.c ml.h util.h puzzle.h ppuzzle.h Makefile $(PCOMPILE) -c $(srcdir)/pstep.c && mv pstep.$(OBJEXT) $@ putil.$(OBJEXT): util.c util.h Makefile $(PCOMPILE) -c $(srcdir)/util.c && mv util.$(OBJEXT) $@ pgamma.$(OBJEXT): gamma.c gamma.h util.h Makefile $(PCOMPILE) -c $(srcdir)/gamma.c && mv gamma.$(OBJEXT) $@ pconsensus.$(OBJEXT): consensus.c consensus.h util.h Makefile $(PCOMPILE) -c $(srcdir)/consensus.c && mv consensus.$(OBJEXT) $@ ptreesort.$(OBJEXT): treesort.c treesort.h util.h Makefile $(PCOMPILE) -c $(srcdir)/treesort.c && mv treesort.$(OBJEXT) $@ ptreetest.$(OBJEXT): treetest.c treetest.h util.h Makefile $(PCOMPILE) -c $(srcdir)/treetest.c && mv treetest.$(OBJEXT) $@ psched.$(OBJEXT): sched.c sched.h ppuzzle.h Makefile $(PCOMPILE) -c $(srcdir)/sched.c && mv sched.$(OBJEXT) $@ ppuzzle.$(OBJEXT): ppuzzle.c ppuzzle.h ml.h util.h puzzle.h gamma.h sched.h Makefile $(PCOMPILE) -c $(srcdir)/ppuzzle.c tree-puzzle-5.2/src/Makefile.in0000644000076400001440000005564310075305505012200 # Makefile.in generated by automake 1.6.1 from Makefile.am. # @configure_input@ # Copyright 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002 # Free Software Foundation, Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, # with or without modifications, as long as this notice is preserved. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY, to the extent permitted by law; without # even the implied warranty of MERCHANTABILITY or FITNESS FOR A # PARTICULAR PURPOSE. @SET_MAKE@ # # Makefile.am # # # Part of TREE-PUZZLE 5.2 (July 2004) # # (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler # (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, # M. Vingron, and Arndt von Haeseler # (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler # # All parts of the source except where indicated are distributed under # the GNU public licence. See http://www.opensource.org for details. # # ($Id$) # SHELL = @SHELL@ srcdir = @srcdir@ top_srcdir = @top_srcdir@ VPATH = @srcdir@ prefix = @prefix@ exec_prefix = @exec_prefix@ bindir = @bindir@ sbindir = @sbindir@ libexecdir = @libexecdir@ datadir = @datadir@ sysconfdir = @sysconfdir@ sharedstatedir = @sharedstatedir@ localstatedir = @localstatedir@ libdir = @libdir@ infodir = @infodir@ mandir = @mandir@ includedir = @includedir@ oldincludedir = /usr/include pkgdatadir = $(datadir)/@PACKAGE@ pkglibdir = $(libdir)/@PACKAGE@ pkgincludedir = $(includedir)/@PACKAGE@ top_builddir = .. ACLOCAL = @ACLOCAL@ AUTOCONF = @AUTOCONF@ AUTOMAKE = @AUTOMAKE@ AUTOHEADER = @AUTOHEADER@ am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd INSTALL = @INSTALL@ INSTALL_PROGRAM = @INSTALL_PROGRAM@ INSTALL_DATA = @INSTALL_DATA@ install_sh_DATA = $(install_sh) -c -m 644 install_sh_PROGRAM = $(install_sh) -c INSTALL_SCRIPT = @INSTALL_SCRIPT@ INSTALL_HEADER = $(INSTALL_DATA) transform = @program_transform_name@ NORMAL_INSTALL = : PRE_INSTALL = : POST_INSTALL = : NORMAL_UNINSTALL = : PRE_UNINSTALL = : POST_UNINSTALL = : EXEEXT = @EXEEXT@ OBJEXT = @OBJEXT@ PATH_SEPARATOR = @PATH_SEPARATOR@ AMTAR = @AMTAR@ AWK = @AWK@ CC = @CC@ DEPDIR = @DEPDIR@ INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@ MPICC = @MPICC@ MPICC0 = @MPICC0@ MPICC1 = @MPICC1@ MPICC2 = @MPICC2@ MPICC3 = @MPICC3@ MPICC4 = @MPICC4@ MPICC5 = @MPICC5@ MPICC6 = @MPICC6@ MPICFLAGS = @MPICFLAGS@ MPIDEFS = @MPIDEFS@ MPILIBS = @MPILIBS@ PACKAGE = @PACKAGE@ PPUZZLE = @PPUZZLE@ STRIP = @STRIP@ VERSION = @VERSION@ am__include = @am__include@ am__quote = @am__quote@ install_sh = @install_sh@ SUBDIRS = sprng bin_PROGRAMS = puzzle @PPUZZLE@ EXTRA_PROGRAMS = ppuzzle EXTRA_DIST = \ pstep-deglob.c\ pstep-deglob.h\ pstep-mrca.c\ pstep-mrca.h\ pstep-orig.c\ pstep-orig.h\ pstep-recursive.c\ pstep-recursive.h\ split.c \ recur.c \ recur-old.c \ mrca.c \ pstep-split.c\ pstep-split.h\ subsetmatr.c\ subsetmatr.h\ pstep-trueID.c\ pstep-trueID.h SPRNG_OBJ = makeseed.$(OBJEXT) store.$(OBJEXT) memory.$(OBJEXT) checkid.$(OBJEXT) lcg64.$(OBJEXT) primes-lcg64.$(OBJEXT) SPRNG_DIR_OBJ = sprng/makeseed.$(OBJEXT) sprng/store.$(OBJEXT) sprng/memory.$(OBJEXT) sprng/checkid.$(OBJEXT) sprng/lcg64.$(OBJEXT) sprng/primes-lcg64.$(OBJEXT) #SPRNG_OBJ = sprng/makeseed.$(OBJEXT) sprng/store.$(OBJEXT) sprng/memory.$(OBJEXT) sprng/checkid.$(OBJEXT) sprng/lcg64.$(OBJEXT) sprng/primes-lcg64.$(OBJEXT) #SPRNG_LFG_SRCS = sprng/lfg.c sprng/interface.h sprng/makeseed.c sprng/memory.c sprng/checkid.c sprng/store.c #SPRNG_LFG_OBJS = sprng/lfg.$(OBJEXT) sprng/makeseed.$(OBJEXT) sprng/memory.$(OBJEXT) sprng/checkid.$(OBJEXT) sprng/store.$(OBJEXT) #SPRNG_MLFG_SRCS = sprng/mlfg.c sprng/interface.h sprng/makeseed.c sprng/memory.c sprng/checkid.c sprng/store.c sprng/int64.h #SPRNG_MLFG_OBJS = sprng/mlfg.$(OBJEXT) sprng/makeseed.$(OBJEXT) sprng/memory.$(OBJEXT) sprng/checkid.$(OBJEXT) sprng/store.$(OBJEXT) #SPRNG_LCG_SRCS = sprng/lcg.c sprng/interface.h sprng/primes-lcg.c sprng/makeseed.c sprng/memory.c sprng/checkid.c sprng/store.c #SPRNG_LCG_OBJS = sprng/lcg.$(OBJEXT) sprng/primes-lcg.$(OBJEXT) sprng/makeseed.$(OBJEXT) sprng/memory.$(OBJEXT) sprng/checkid.$(OBJEXT) sprng/store.$(OBJEXT) #SPRNG_CMRG_SRCS = sprng/lcg64.c sprng/interface.h sprng/primes-lcg64.c sprng/makeseed.c sprng/memory.c sprng/checkid.c sprng/store.c #SPRNG_CMRG_OBJS = sprng/lcg64.$(OBJEXT) sprng/primes-lcg64.$(OBJEXT) sprng/makeseed.$(OBJEXT) sprng/memory.$(OBJEXT) sprng/checkid.$(OBJEXT) sprng/store.$(OBJEXT) #SPRNG_LCG64_SRCS = sprng/lcg64.c sprng/interface.h sprng/primes-lcg64.c sprng/makeseed.c sprng/memory.c sprng/checkid.c sprng/store.c #SPRNG_LCG64_OBJS = sprng/lcg64.$(OBJEXT) sprng/primes-lcg64.$(OBJEXT) sprng/makeseed.$(OBJEXT) sprng/memory.$(OBJEXT) sprng/checkid.$(OBJEXT) sprng/store.$(OBJEXT) puzzle_SOURCES = gamma.c ml1.c ml2.c mlparam.c model1.c model2.c puzzle1.c puzzle2.c pstep.c util.c consensus.c treesort.c treetest.c ml.h util.h puzzle.h pstep.h gamma.h consensus.h treesort.h treetest.h #puzzle_LDADD = sgamma.o sml1.o sml2.o smlparam.o smodel1.o smodel2.o spuzzle1.o spuzzle2.o spstep.o sutil.o sconsensus.o streesort.o sprng/liblcg64.a puzzle_LDADD = sgamma.$(OBJEXT) sml1.$(OBJEXT) sml2.$(OBJEXT) smlparam.$(OBJEXT) smodel1.$(OBJEXT) smodel2.$(OBJEXT) spuzzle1.$(OBJEXT) spuzzle2.$(OBJEXT) spstep.$(OBJEXT) sutil.$(OBJEXT) sconsensus.$(OBJEXT) streesort.$(OBJEXT) streetest.$(OBJEXT) INCLUDES = -I. -I.. -I$(srcdir) -I$(srcdir)/sprng SDEFS = SCFLAGS = SLDFLAGS = SLDLIBS = @LIBS@ SCOMPILE = $(CC) $(SDEFS) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(SCFLAGS) $(CFLAGS) SCCLD = $(CC) SLINK = $(SCCLD) $(AM_CFLAGS) $(CFLAGS) $(SLDFLAGS) $(LDFLAGS) ppuzzle_SOURCES = gamma.c ml1.c ml2.c mlparam.c model1.c model2.c puzzle1.c puzzle2.c pstep.c sched.c util.c consensus.c treesort.c treetest.c ppuzzle.c ml.h util.h puzzle.h pstep.h gamma.h ppuzzle.h sched.h consensus.h treesort.h treetest.h ppuzzle_LDADD = pgamma.$(OBJEXT) pml1.$(OBJEXT) pml2.$(OBJEXT) pmlparam.$(OBJEXT) pmodel1.$(OBJEXT) pmodel2.$(OBJEXT) ppuzzle1.$(OBJEXT) ppuzzle2.$(OBJEXT) ppstep.$(OBJEXT) psched.$(OBJEXT) putil.$(OBJEXT) pconsensus.$(OBJEXT) ptreesort.$(OBJEXT) ptreetest.$(OBJEXT) ppuzzle.$(OBJEXT) PCC = @MPICC@ PDEFS = -DPARALLEL PCFLAGS = PLDFLAGS = PLDLIBS = @LIBS@ @MPILIBS@ PCOMPILE = $(PCC) $(PDEFS) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(PCFLAGS) $(CFLAGS) PCCLD = $(PCC) PLINK = $(PCCLD) $(AM_CFLAGS) $(PCFLAGS) $(CFLAGS) $(PLDFLAGS) $(LDFLAGS) subdir = src mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs CONFIG_HEADER = config.h CONFIG_CLEAN_FILES = EXTRA_PROGRAMS = ppuzzle$(EXEEXT) bin_PROGRAMS = puzzle$(EXEEXT) @PPUZZLE@ PROGRAMS = $(bin_PROGRAMS) am_ppuzzle_OBJECTS = gamma.$(OBJEXT) ml1.$(OBJEXT) ml2.$(OBJEXT) \ mlparam.$(OBJEXT) model1.$(OBJEXT) model2.$(OBJEXT) \ puzzle1.$(OBJEXT) puzzle2.$(OBJEXT) pstep.$(OBJEXT) \ sched.$(OBJEXT) util.$(OBJEXT) consensus.$(OBJEXT) \ treesort.$(OBJEXT) treetest.$(OBJEXT) ppuzzle.$(OBJEXT) ppuzzle_OBJECTS = $(am_ppuzzle_OBJECTS) ppuzzle_DEPENDENCIES = pgamma.$(OBJEXT) pml1.$(OBJEXT) pml2.$(OBJEXT) \ pmlparam.$(OBJEXT) pmodel1.$(OBJEXT) pmodel2.$(OBJEXT) \ ppuzzle1.$(OBJEXT) ppuzzle2.$(OBJEXT) ppstep.$(OBJEXT) \ psched.$(OBJEXT) putil.$(OBJEXT) pconsensus.$(OBJEXT) \ ptreesort.$(OBJEXT) ptreetest.$(OBJEXT) ppuzzle.$(OBJEXT) ppuzzle_LDFLAGS = am_puzzle_OBJECTS = gamma.$(OBJEXT) ml1.$(OBJEXT) ml2.$(OBJEXT) \ mlparam.$(OBJEXT) model1.$(OBJEXT) model2.$(OBJEXT) \ puzzle1.$(OBJEXT) puzzle2.$(OBJEXT) pstep.$(OBJEXT) \ util.$(OBJEXT) consensus.$(OBJEXT) treesort.$(OBJEXT) \ treetest.$(OBJEXT) puzzle_OBJECTS = $(am_puzzle_OBJECTS) puzzle_DEPENDENCIES = sgamma.$(OBJEXT) sml1.$(OBJEXT) sml2.$(OBJEXT) \ smlparam.$(OBJEXT) smodel1.$(OBJEXT) smodel2.$(OBJEXT) \ spuzzle1.$(OBJEXT) spuzzle2.$(OBJEXT) spstep.$(OBJEXT) \ sutil.$(OBJEXT) sconsensus.$(OBJEXT) streesort.$(OBJEXT) \ streetest.$(OBJEXT) puzzle_LDFLAGS = DEFS = @DEFS@ DEFAULT_INCLUDES = -I. -I$(srcdir) -I. 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Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ /* initialize tree with the following starting configuration (see pstep.h) */ void inittree_mrca(ONEEDGE **edge, /* out: new array of edges */ int **edgeofleaf,/* out: array of external edge ptrs */ int *rootleaf, /* out: rooting leaf (=trueID[0]) */ int Maxspc, /* in: Number of species (n) */ int Maxbrnch, /* in: Number of branches (2n-3) */ int *nextedge, /* out: next free edge index (=3) */ int *nextleaf, /* out: next free leaf index (=3) */ int *trueID, imatrix mrcamatrix) { int i, j; ONEEDGE *tmpedge; int *tmpedgeofleaf; /* allocate the memory for the whole tree */ /* allocate memory for vector with all the edges of the tree */ tmpedge = (ONEEDGE *) calloc((size_t) Maxbrnch, sizeof(ONEEDGE) ); if (tmpedge == NULL) maerror("edge in inittree"); *edge = tmpedge; /* allocate memory for tmpvector with edge numbers of leaves */ tmpedgeofleaf = (int *) calloc((size_t) Maxspc, sizeof(int) ); if (tmpedgeofleaf == NULL) maerror("edgeofleaf in inittree"); for (j = 0; j < Maxspc; j++) tmpedgeofleaf[j]=-1; *edgeofleaf = tmpedgeofleaf; /* allocate memory for all the edges the split map */ for (i = 0; i < Maxbrnch; i++) { (tmpedge)[i].cluster = (int *) calloc((size_t) Maxspc, sizeof(int) ); if (tmpedge[i].cluster == NULL) maerror("edge cluster array in inittree"); (tmpedge)[i].penaltyprop = (uli *) calloc((size_t) Maxspc, sizeof(uli) ); if (tmpedge[i].penaltyprop == NULL) maerror("edge penalty propagation array in inittree"); (tmpedge)[i].taxon = -1; for (j = 0; j < Maxspc; j++) { (tmpedge)[i].cluster[j]=-1; (tmpedge)[i].penaltyprop[j]=0; } /* number all edges */ tmpedge[i].numedge = i; } /* initialize tree */ *nextedge = 3; *nextleaf = 3; /* uppest edge =: root edge*/ *rootleaf = trueID[0]; /* init cluster vectors: */ /* for edge 0 */ (tmpedge[0].cluster)[0] = trueID[1]; /* leaf 1 in edge cluster */ (tmpedge[0].cluster)[1] = trueID[2]; /* leaf 2 in edge cluster */ tmpedge[0].clsize = 2; /* for edge 1 */ (tmpedge[1].cluster)[0] = trueID[1]; /* leaf 0 in edge cluster */ tmpedge[1].clsize = 1; /* for edge 2 */ (tmpedge[2].cluster)[0] = trueID[2]; /* leaf 0 in edge cluster */ tmpedge[2].clsize = 1; /* initializing mrca marix */ for (i=0; i < Maxspc; i++) { mrcamatrix[*rootleaf][i] = 0; mrcamatrix[i][*rootleaf] = 0; } mrcamatrix[trueID[1]][trueID[2]] = 0; mrcamatrix[trueID[2]][trueID[1]] = 0; /* debug */ mrcamatrix[trueID[1]][trueID[1]] = -8; mrcamatrix[trueID[2]][trueID[2]] = -8; /* interconnection */ tmpedge[0].up = NULL; tmpedge[0].downleft = &tmpedge[1]; tmpedge[0].downright = &tmpedge[2]; tmpedge[1].up = &tmpedge[0]; tmpedge[1].downleft = NULL; tmpedge[1].downright = NULL; tmpedge[2].up = &tmpedge[0]; tmpedge[2].downleft = NULL; tmpedge[2].downright = NULL; /* taxon IDs of leaves */ tmpedge[0].taxon = trueID[0]; tmpedge[1].taxon = trueID[1]; tmpedge[2].taxon = trueID[2]; /* edges of leaves */ tmpedgeofleaf[trueID[0]] = 0; tmpedgeofleaf[trueID[1]] = 1; tmpedgeofleaf[trueID[2]] = 2; } /* inittree_mrca */ /******************/ /* free memory (to be called after inittree) */ void freetree_mrca(ONEEDGE *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc) /* No. of species */ { int i; /* free vectors */ for (i = 0; i < 2 * Maxspc - 3; i++) { free(edge[i].cluster); free(edge[i].penaltyprop); } /* free tree topology */ free(edge); /* free external edge lookup vector */ free(edgeofleaf); } /* freetree_mrca */ /******************/ void updatecluster_mrca(ONEEDGE *curredge, /* current edge */ int wherefrom, /* direction to last curr. edge */ int newleaf, /* leaf to add to clusters */ ONEEDGE *edge, /* edge array */ int Maxspc, /* No. of species */ int Maxbrnch, /* No. of branches */ int *edgeofleaf, /* ext. edge idx array */ int in_nextedge, /* next free edge idx */ int in_nextleaf, /* next free leaf idx */ imatrix mrcamatrix) { int n, edgenum, clsize, leaf; ONEEDGE *branchedge; if (wherefrom == DOWNLEFT) branchedge = curredge->downright; else branchedge = curredge->downleft; edgenum = curredge->numedge; clsize = branchedge->clsize; for (n=0; ncluster[n]; mrcamatrix[newleaf][leaf] = edgenum; mrcamatrix[leaf][newleaf] = edgenum; } curredge->cluster[(curredge->clsize)++] = newleaf; /* newleaf is down */ if ((curredge->up) != NULL) { /* not root */ if (((curredge->up)->downright) == curredge) { wherefrom = DOWNRIGHT; } else { wherefrom = DOWNLEFT; } updatecluster_mrca(curredge->up, wherefrom, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf, mrcamatrix); } } /* updatecluster_mrca */ /******************/ /* add next leaf on the specified edge */ void updatetreeclusters_mrca(int dockedge, /* dockedge */ int newleaf, /* leaf to add to clusters */ ONEEDGE *edge, /* edge array */ int rootleaf, /* root leaf */ int Maxspc, /* No. of species */ int *edgeofleaf, /* ext. edge idx array */ int in_nextedge, /* next free edge idx */ int in_nextleaf, /* next free leaf idx */ ivector permut, imatrix mrcamatrix) { int n; /* counter */ int wherefrom; /* direction to last edge */ ONEEDGE *curredge; /* edge array */ /* copy cluster dockedge -> nextedge */ for (n=0; n < edge[dockedge].clsize; n++) { (edge[in_nextedge]).cluster[n] = (edge[dockedge]).cluster[n]; } if (&(edge[in_nextedge]) != &(edge[edgeofleaf[rootleaf]])) { #if 0 mrcamatrix[rootleaf][newleaf] = in_nextedge; mrcamatrix[newleaf][rootleaf] = in_nextedge; #endif } else { for (n=0; n < Maxspc; n++) { mrcamatrix[rootleaf][n] = in_nextedge; mrcamatrix[n][rootleaf] = in_nextedge; } } /* set new internal edge's (nextedge) cluster size */ (edge[in_nextedge]).clsize = (edge[dockedge]).clsize; /* add newleaf new external edge's (nextedge+1) cluster */ (edge[in_nextedge + 1]).cluster[0] = newleaf; (edge[in_nextedge + 1]).clsize = 1; curredge = &(edge[in_nextedge+1]); if (curredge->up != NULL) { /* not root */ if (((curredge->up)->downright) == curredge) { wherefrom = DOWNRIGHT; } else { wherefrom = DOWNLEFT; } /* climbing up from insertion point */ updatecluster_mrca(curredge->up, DOWNRIGHT, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf, mrcamatrix); } } /* updatetreeclusters_mrca */ /******************/ #if 0 void updatesplit_split(ONEEDGE *curredge, /* current edge */ int wherefrom, /* direction to last curr. edge */ int newleaf, /* leaf to add to splits */ ONEEDGE *edge, /* edge array */ int Maxspc, /* No. of species */ int Maxbrnch, /* No. of branches */ int *edgeofleaf, /* ext. edge idx array */ int in_nextedge, /* next free edge idx */ int in_nextleaf) /* next free leaf idx */ { switch (wherefrom) { case UP: curredge->split[(curredge->upsize)++] = newleaf; /* leaf is up */ if (curredge->downright != NULL) { /* not leaf */ updatesplit_split(curredge->downright, UP, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); updatesplit_split(curredge->downleft, UP, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } else { /* nothing to do */ return; } break; case DOWNLEFT: curredge->split[Maxspc - ++(curredge->downsize)] = newleaf; /* leaf is down */ if (curredge->downright != NULL) { /* not leaf */ updatesplit_split(curredge->downright, UP, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } if (curredge->up != NULL) { /* not root */ if ((curredge->up)->downright == curredge) { updatesplit_split(curredge->up, DOWNRIGHT, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } else { updatesplit_split(curredge->up, DOWNLEFT, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } } break; case DOWNRIGHT: curredge->split[Maxspc - ++(curredge->downsize)] = newleaf; /* leaf is down */ if (curredge->downright != NULL) { /* not leaf */ updatesplit_split(curredge->downleft, UP, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } if ((curredge->up) != NULL) { /* not root */ if ((curredge->up)->downright == curredge) { updatesplit_split(curredge->up, DOWNRIGHT, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } else { updatesplit_split(curredge->up, DOWNLEFT, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } } break; } } /* updatesplit_split */ /******************/ /* add next leaf on the specified edge */ void updatetreesplits_split(int dockedge, /* dockedge */ int newleaf, /* leaf to add to splits */ ONEEDGE *edge, /* edge array */ int Maxspc, /* No. of species */ int *edgeofleaf, /* ext. edge idx array */ int in_nextedge, /* next free edge idx */ int in_nextleaf, /* next free leaf idx */ ivector permut) { int n; /* counter */ int wherefrom; /* direction to last edge */ ONEEDGE *curredge; /* edge array */ /* copy clusters from dockedge to in_nextedge */ /* up-cluster: upsize-1 .. 0 */ for (n=(edge[dockedge].upsize) - 1; n >= 0; n--) { (edge[in_nextedge]).split[n] = (edge[dockedge]).split[n]; } (edge[in_nextedge]).upsize = (edge[dockedge]).upsize; /* down-cluster: downsize .. Maxspc-1 */ for (n=Maxspc - (edge[dockedge]).downsize; n < Maxspc; n++) { (edge[in_nextedge]).split[n] = (edge[dockedge]).split[n]; } (edge[in_nextedge]).downsize = (edge[dockedge]).downsize; /* add the new taxon to in_nextedge */ (edge[in_nextedge]).split[Maxspc - ++((edge[in_nextedge]).downsize)] = permut[in_nextleaf]; /* setup clusters for new external edge (in_nextedge+1) */ /* up-cluster: all taxa in tree */ for (n=0; n < in_nextleaf; n++) { (edge[in_nextedge+1]).split[n] = permut[n]; } (edge[in_nextedge+1]).upsize = in_nextleaf; /* down-cluster: the new taxon itself */ (edge[in_nextedge+1]).split[Maxspc-1] = permut[in_nextleaf]; (edge[in_nextedge+1]).downsize = 1; curredge = &(edge[in_nextedge]); if (curredge->up != NULL) { /* not root */ if (((curredge->up)->downright) == curredge) { wherefrom = DOWNRIGHT; } else { wherefrom = DOWNLEFT; } /* climbing up from insertion point */ updatesplit_split(curredge->up, wherefrom, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } /* climbing down to dockedge from insertion point */ updatesplit_split(&(edge[dockedge]), UP, newleaf, edge, Maxspc, Maxbrnch, edgeofleaf, in_nextedge, in_nextleaf); } /* updatetreesplits_split */ #endif /******************/ /* add next leaf on the specified edge */ void addnextleaf_mrca(int dockedge, /* insert here */ ONEEDGE *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int rootleaf, /* uppest leaf */ int Maxspc, /* No. of species */ int Maxbrnch, /* No. of branches */ int *in_nextedge, /* next free edge idx */ int *in_nextleaf, /* next free leaf idx */ ivector permut, imatrix mrcamatrix) /* MRCA matrix */ { int nextedge; int nextleaf; nextedge=*in_nextedge; nextleaf=*in_nextleaf; if (dockedge >= nextedge) { /* Trying to add leaf nextleaf to nonexisting edge dockedge */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR F TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } if (nextleaf >= Maxspc) { /* Trying to add leaf nextleaf to a tree with Maxspc leaves */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR G TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } /* necessary change in edgeofleaf if dockedge == root edge */ if (edgeofleaf[rootleaf] == dockedge) edgeofleaf[rootleaf] = nextedge; /* adding nextedge to the tree */ edge[nextedge].up = edge[dockedge].up; edge[nextedge].downleft = &edge[dockedge]; edge[nextedge].downright = &edge[nextedge+1]; edge[dockedge].up = &edge[nextedge]; /* if not root edge: connect ancestor to internal edge (nextedge) */ if (edge[nextedge].up != NULL) { if ( ((edge[nextedge].up)->downleft) == &edge[dockedge] ) (edge[nextedge].up)->downleft = &edge[nextedge]; else (edge[nextedge].up)->downright = &edge[nextedge]; } /* adding new external edge (nextedge+1) to the tree */ edge[nextedge+1].up = &edge[nextedge]; edge[nextedge+1].downleft = NULL; edge[nextedge+1].downright = NULL; edge[nextedge+1].taxon = permut[nextleaf]; edgeofleaf[permut[nextleaf]] = nextedge+1; #if 0 updatetreesplits_split(dockedge, permut[nextleaf], edge, Maxspc, edgeofleaf, nextedge, nextleaf, permut); #endif updatetreeclusters_mrca(dockedge, permut[nextleaf], edge, rootleaf, Maxspc, edgeofleaf, nextedge, nextleaf, permut, mrcamatrix); (*in_nextedge) += 2; (*in_nextleaf) ++; } /* addnextleaf_mrca */ /******************/ /* compute edge penalties using splits, if #minedges>1 choose one randomly */ void computepenalties_mrca(ONEEDGE *curredge, /* edge array */ int Maxspc, /* number of taxa */ imatrix mrcamatrix, /* MRCA matrix */ int *minedges, /* minimum edge vector */ int *howmany, /* number minimum edge */ uli *minpenalty) /* minimum penalty */ { int l, r; int lmax, rmax; int taxon; ONEEDGE *left; /* temp edge ptr */ ONEEDGE *right; /* temp edge ptr */ if (curredge->downleft == NULL) { /* leaf edge */ /* check for new minimal panalty */ if (*minpenalty == curredge->edgeinfo) { /* another min edge */ minedges[(*howmany)++] = curredge->numedge; } else { /* -> not same minimum */ if (*minpenalty > curredge->edgeinfo) { /* new minimum penalty */ *howmany = 1; minedges[0] = curredge->numedge; *minpenalty = curredge->edgeinfo; } /* if new minimum */ } /* same minimum */ } else { /* -> internal edge */ /* propagate to left child */ left = curredge->downleft; lmax = left->clsize; left->edgeinfo = 0; for (l= 0; lcluster[l]; left->edgeinfo += curredge->penaltyprop[taxon]; left->penaltyprop[taxon] += curredge->penaltyprop[taxon]; } /* propagate to right child */ right = curredge->downright; rmax = right->clsize; right->edgeinfo = 0; for (r= 0; rcluster[r]; right->edgeinfo += curredge->penaltyprop[taxon]; right->penaltyprop[taxon] += curredge->penaltyprop[taxon]; } /* descend downleft */ computepenalties_mrca(left, Maxspc, mrcamatrix, minedges, howmany, minpenalty); /* descend downright */ computepenalties_mrca(right, Maxspc, mrcamatrix, minedges, howmany, minpenalty); if (*minpenalty == curredge->edgeinfo) { /* another min edge */ minedges[(*howmany)++] = curredge->numedge; } else { /* -> not same minimum */ if (*minpenalty > curredge->edgeinfo) { /* new minimum penalty */ *howmany = 1; minedges[0] = curredge->numedge; *minpenalty = curredge->edgeinfo; } /* if new minimum */ } /* same minimum */ ; } } /* computepenalties_mrca */ /******************/ /* compute edge penalties using splits, if #minedges>1 choose one randomly */ void computepenaltiestree_mrca(ONEEDGE *tmpedge, /* edge array */ int *edgeofleaf, /* external edge ptrs */ int rootleaf, /* idx of uppest edge */ int nextleaf, /* next free leaf idx */ int Maxspc, /* number of taxa */ imatrix mrcamatrix, /* MRCA matrix */ int *minedges, /* minimum edge vector */ int *out_howmany, /* number minimum edge */ uli *out_minpenalty, /* minimum penalty */ int *out_minedge) /* minimum edge */ { int rootedge; int taxon; int lmax, rmax; int l, r; int howmany = 0; ONEEDGE *left; /* temp edge ptr */ ONEEDGE *right; /* temp edge ptr */ uli minpenalty; uli edgeinfo; ONEEDGE *curredge; rootedge = edgeofleaf[rootleaf]; curredge = &(tmpedge[rootedge]); curredge->edgeinfo = curredge->penaltyprop[rootleaf]; if (minedges == NULL) minedges = (int *) calloc((size_t) Maxspc, sizeof(int)); /* first edge: init */ minedges[0] = rootedge; howmany = 1; minpenalty = curredge->edgeinfo; edgeinfo = 0; for (l= 0; lpenaltyprop)[curredge->cluster[l]]; } #if 0 if ((edgeinfo) != (curredge->edgeinfo)) fprintf(stderr, "%ld != %ld\n", edgeinfo, curredge->edgeinfo); else fprintf(stderr, "%ld == %ld\n", edgeinfo, curredge->edgeinfo); if ((edgeinfo) != (curredge->edgeinfo)) { /* root edge cluster penalty should be equal to root penalty */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR HSCL2 TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } #endif /* propagate to left child */ left = curredge->downleft; lmax = left->clsize; left->edgeinfo = 0; for (l= 0; lcluster[l]; left->edgeinfo += curredge->penaltyprop[taxon]; left->penaltyprop[taxon] += curredge->penaltyprop[taxon]; } /* propagate to right child */ right = curredge->downright; rmax = right->clsize; right->edgeinfo = 0; for (r= 0; rcluster[r]; right->edgeinfo += curredge->penaltyprop[taxon]; right->penaltyprop[taxon] += curredge->penaltyprop[taxon]; } if ((lmax + rmax) != (nextleaf-1)) { /* root edge cluster should yield all other leaves */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR HSCL1 TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } /* descend downleft */ computepenalties_mrca(left, Maxspc, mrcamatrix, minedges, &howmany, &minpenalty); /* descend downright */ computepenalties_mrca(right, Maxspc, mrcamatrix, minedges, &howmany, &minpenalty); #if 0 /* optimization (HAS) */ if (howmany > 1) *out_minedge = minedges[randominteger(howmany)]; else *out_minedge = minedges[0]; #endif if (howmany > 1) { /* draw random edge */ int i, k, randomnum; randomnum = randominteger(howmany) + 1; /* 1 to howmany */ i = -1; for (k = 0; k < randomnum; k++) { do { i++; } while (tmpedge[i].edgeinfo != minpenalty); *out_minedge = tmpedge[i].numedge; } } else { *out_minedge = minedges[0]; } *out_howmany = howmany; *out_minpenalty = minpenalty; } /* computepenaltiestree_mrca */ /******************/ #if 0 /* compute edge penalties using splits, if #minedges>1 choose one randomly */ void computepenalties_split(ONEEDGE *tmpedge, /* edge array */ int nextedge, /* next free edge idx */ int Maxspc, /* number of taxa */ ulimatrix neighbormatr, /* neighborhood matrix */ int **out_minedges, /* minimum edge vector */ int *out_howmany, /* number minimum edge */ uli *out_minpenalty, /* minimum penalty */ int *out_minedge) /* minimum edge */ { int i; /* counter */ int a, b; int idxA, idxB; int maxUP; /* index counter for right/left split cluster */ int howmany = 0; int *minedges = *out_minedges; uli minpenalty; for (i = 0; i < nextedge; i++) { (tmpedge[i]).penalty = 0; /* reset penalty */ maxUP = (tmpedge[i]).upsize; for (idxB = Maxspc - (tmpedge[i]).downsize; idxB < Maxspc; idxB++) { b = (tmpedge[i].split)[idxB]; for (idxA = 0; idxA < maxUP; idxA++) { a = (tmpedge[i].split)[idxA]; (tmpedge[i]).penalty += neighbormatr[a][b]; } /* for all root-sided (up) taxa */ } /* for all non-root-sided (down) taxa */ if (howmany == 0) { /* first edge: init */ if (minedges == NULL) minedges = (int *) calloc((size_t) Maxspc, sizeof(int)); minedges[howmany++] = i; minpenalty = tmpedge[i].penalty; } else { /* -> all other edges */ if (minpenalty == tmpedge[i].penalty) { /* another min edge */ minedges[howmany++] = i; } else { /* -> not same minimum */ if (minpenalty > tmpedge[i].penalty) { /* new minimum penalty */ howmany = 0; minedges[howmany++] = i; minpenalty = tmpedge[i].penalty; } /* if new minimum */ } /* same minimum */ } /* if all other edges */ } /* for all edges */ *out_howmany = howmany, *out_minpenalty = minpenalty; #if 0 if (howmany > 1) *out_minedge = minedges[0]; else *out_minedge = minedges[0]; #endif } /* computepenalties_split */ #endif /******************/ /* trueID-ed (HAS) */ /* perform one single puzzling step to produce one intermediate tree */ void onepstep_mrca( /* PStep (intermediate) tree topol: */ ONEEDGE **edge, /* out: new array of edges */ int **edgeofleaf, /* out: array of extern edge ptrs */ int *rootleaf, /* out: root leaf in topol, starting perm[0] */ unsigned char *quartettopols, /* in: quartetblock with all topols */ int Maxspc, /* in: Number of species (n) */ ivector permut) /* in: species permutation (trueID) */ { /* local variables: */ int Maxbrnch = (2*Maxspc)-3; /* Number of branches (2n-3) */ int nextedge; /* next free edge index (=3) */ int nextleaf; /* next free leaf index (=3) */ int minedge; /* insertion edge of minimum penalty */ uli mininfo; /* minimum penalty */ int a, b, c, i; /* quartet leaves, i to be inserted */ int idxA, idxB; int idxC, idxI; /* index counter for quartet leaves */ int chooseX, chooseY; /* end leaves of penalty path */ ONEEDGE *tmpedge; /* new array of edges */ int *tmpedgeofleaf; /* array of extern edge ptrs */ int tmprootleaf; /* root edge */ imatrix mrcamatrix; int mrca; int *minedges; int howmany; #if 0 ulimatrix neighbormatr; neighbormatr = new_ulimatrix(Maxspc,Maxspc); #endif minedges = (int *) calloc((size_t) Maxspc, sizeof(int)); if (minedges == NULL) maerror("minimal edge set in onepstep_mrca"); mrcamatrix = new_imatrix(Maxspc,Maxspc); /* allocate and initialize new tree topology */ inittree_mrca(&tmpedge, &tmpedgeofleaf, &tmprootleaf, Maxspc, Maxbrnch, &nextedge, &nextleaf, permut, mrcamatrix); /* check_mrca(tmpedge, Maxspc, tmpedgeofleaf, nextedge, nextleaf, permut); */ for (idxI = 3; idxI < Maxspc; idxI++) { i = permut[idxI]; #if 0 fprintf(stderr, "----------------------------------------------\n"); fprintf(stderr, " %d. adding taxon %d \n", idxI, i); fprintf(stderr, "----------------------------------------------\n"); /* initialize penalty neighborhood matrix + leafpenalty vector */ for (idxA = 0; idxA < nextleaf - 1; idxA++) { a = permut[idxA]; for (idxB = idxA + 1; idxB < nextleaf; idxB++) { b = permut[idxB]; neighbormatr[a][b] = 0; neighbormatr[b][a] = 0; } } /* for all entries in the upper neighbormatr */ #endif /* * core of quartet puzzling algorithm */ for (idxA = 0; idxA < nextleaf - 2; idxA++) { a = permut[idxA]; for (idxB = idxA + 1; idxB < nextleaf - 1; idxB++) { b = permut[idxB]; for (idxC = idxB + 1; idxC < nextleaf; idxC++) { c = permut[idxC]; /* check which two leaves out of a,b,c are closer related to each other than to leaf i according to a least squares fit of the continous Bayesian weights to the seven trivial "attractive regions". We assign a score of 1 to all edges on the penalty path between these two leaves chooseX and chooseY */ /* de-trueID-ed (HAS) */ checkquartet(a, b, c, i, &chooseX, &chooseY); #if 0 (neighbormatr[chooseX][chooseY])++; (neighbormatr[chooseY][chooseX])++; #endif mrca = mrcamatrix[chooseX][chooseY]; (tmpedge[mrca].penaltyprop[chooseX])++; (tmpedge[mrca].penaltyprop[chooseY])++; } /* for all quartets q=(a,b,c,i): c */ } /* for all quartets q=(a,b,c,i): b */ } /* for all quartets q=(a,b,c,i): a */ #if 0 computepenalties_split(tmpedge, nextedge, Maxspc, neighbormatr, &minedges, &howmany, &mininfo, &minedge); {int m,n; for (m=0; m #endif /* * Use Scalable Parallel Random Number Generator * See sprng.cs.fsu.edu for details * from National Center for Supercomputing Applications (NCSA) * See www.ncsa.uiuc.edu */ #ifdef NOSPRNG # ifdef SPRNG # undef SPRNG # endif #else # define SPRNG 1 #endif #ifdef SPRNG # ifdef PARALLEL # define USE_MPI # ifndef EXTERN # define EXTERN extern # endif # include "ppuzzle.h" # endif # if 0 # define SIMPLE_SPRNG # endif # include "sprng/sprng.h" #endif #include "util.h" #define STDOUT stdout #ifndef PARALLEL /* because printf() runs significantly faster */ /* than fprintf(stdout) on an Apple McIntosh */ /* (HS) */ # define FPRINTF printf # define STDOUTFILE #else # define FPRINTF fprintf # define STDOUTFILE STDOUT, extern int PP_NumProcs; extern int PP_Myid; long int PP_randn; long int PP_rand; void PP_Finalize(); #endif /********************************** * memory allocation error handler */ void maerror(char *message) { fprintf(STDOUT, "\n\n\nUnable to proceed (lack of memory: %s)\n\n", message); fprintf(STDOUT, "Hint for Macintosh users:\n"); fprintf(STDOUT, "Use the command of the Finder to increase the memory partition!\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } /* maerror */ /****************************************************** * memory allocate double vectors, matrices, and cubes */ dvector new_dvector(int n) { dvector v; v = (dvector) calloc((size_t) n, sizeof(double)); if (v == NULL) maerror("step 1 in new_dvector"); return v; } /* new_dvector */ /******************/ dmatrix new_dmatrix(int nrow, int ncol) { int i; dmatrix m; m = (dmatrix) calloc((size_t) nrow, sizeof(dvector)); if (m == NULL) maerror("step 1 in in new_dmatrix"); *m = (dvector) calloc((size_t) (nrow * ncol), sizeof(double)); if (*m == NULL) maerror("step 2 in in new_dmatrix"); for (i = 1; i < nrow; i++) m[i] = m[i-1] + ncol; return m; } /* new_dmatrix */ /******************/ dcube new_dcube(int ntri, int nrow, int ncol) { int i, j; dcube c; c = (dcube) calloc((size_t) ntri, sizeof(dmatrix)); if (c == NULL) maerror("step 1 in in new_dcube"); *c = (dmatrix) calloc((size_t) (ntri * nrow), sizeof(dvector)); if (*c == NULL) maerror("step 2 in in new_dcube"); **c = (dvector) calloc((size_t) (ntri * nrow * ncol), sizeof(double)); if (**c == NULL) maerror("step 3 in in new_dcube"); for (j = 1; j < nrow; j++) c[0][j] = c[0][j-1] + ncol; for (i = 1; i < ntri; i++) { c[i] = c[i-1] + nrow; c[i][0] = c[i-1][0] + nrow * ncol; for (j = 1; j < nrow; j++) c[i][j] = c[i][j-1] + ncol; } return c; } /* new_dcube */ /******************/ void free_dvector(dvector v) { free((double *) v); } /* free_dvector */ /******************/ void free_dmatrix(dmatrix m) { free((double *) *m); free((double *) m); } /* free_dmatrix */ /******************/ void free_dcube(dcube c) { free((double *) **c); free((double *) *c); free((double *) c); } /* free_dcube */ /**************************************************** * memory allocate char vectors, matrices, and cubes */ cvector new_cvector(int n) { cvector v; v = (cvector) calloc((size_t) n, sizeof(char)); if (v == NULL) maerror("step1 in new_cvector"); return v; } /* new_cvector */ /******************/ cmatrix new_cmatrix(int nrow, int ncol) { int i; cmatrix m; m = (cmatrix) calloc((size_t) nrow, sizeof(cvector)); if (m == NULL) maerror("step 1 in new_cmatrix"); *m = (cvector) calloc((size_t) (nrow * ncol), sizeof(char)); if (*m == NULL) maerror("step 2 in new_cmatrix"); for (i = 1; i < nrow; i++) m[i] = m[i-1] + ncol; return m; } /* new_cmatrix */ /******************/ ccube new_ccube(int ntri, int nrow, int ncol) { int i, j; ccube c; c = (ccube) calloc((size_t) ntri, sizeof(cmatrix)); if (c == NULL) maerror("step 1 in new_ccube"); *c = (cmatrix) calloc((size_t) (ntri * nrow), sizeof(cvector)); if (*c == NULL) maerror("step 2 in new_ccube"); **c = (cvector) calloc((unsigned) (ntri * nrow * ncol), sizeof(char)); if (**c == NULL) maerror("step 3 in new_ccube"); for (j = 1; j < nrow; j++) c[0][j] = c[0][j-1] + ncol; for (i = 1; i < ntri; i++) { c[i] = c[i-1] + nrow; c[i][0] = c[i-1][0] + nrow * ncol; for (j = 1; j < nrow; j++) c[i][j] = c[i][j-1] + ncol; } return c; } /* new_ccube */ /******************/ void free_cvector(cvector v) { free((char *) v); } /* free_cvector */ /******************/ void free_cmatrix(cmatrix m) { free((char *) *m); free((char *) m); } /* free_cmatrix */ /******************/ void free_ccube(ccube c) { free((char *) **c); free((char *) *c); free((char *) c); } /* free_ccube */ /*************************************************** * memory allocate int vectors, matrices, and cubes */ ivector new_ivector(int n) { ivector v; v = (ivector) calloc((size_t) n, sizeof(int)); if (v == NULL) maerror("step 1 in new_ivector"); return v; } /* new_ivector */ /******************/ imatrix new_imatrix(int nrow, int ncol) { int i; imatrix m; m = (imatrix) calloc((size_t) nrow, sizeof(ivector)); if (m == NULL) maerror("step 1 in new_imatrix"); *m = (ivector) calloc((size_t) (nrow * ncol), sizeof(int)); if (*m == NULL) maerror("step 2 in new_imatrix"); for (i = 1; i < nrow; i++) m[i] = m[i-1] + ncol; return m; } /* new_imatrix */ /******************/ icube new_icube(int ntri, int nrow, int ncol) { int i, j; icube c; c = (icube) calloc((size_t) ntri, sizeof(imatrix)); if (c == NULL) maerror("step 1 in new_icube"); *c = (imatrix) calloc((size_t) (ntri * nrow), sizeof(ivector)); if (*c == NULL) maerror("step 2 in new_icube"); **c = (ivector) calloc((size_t) (ntri * nrow * ncol), sizeof(int)); if (**c == NULL) maerror("step 3 in new_icube"); for (j = 1; j < nrow; j++) c[0][j] = c[0][j-1] + ncol; for (i = 1; i < ntri; i++) { c[i] = c[i-1] + nrow; c[i][0] = c[i-1][0] + nrow * ncol; for (j = 1; j < nrow; j++) c[i][j] = c[i][j-1] + ncol; } return c; } /* new_icube */ /******************/ void free_ivector(ivector v) { free((int *) v); } /* free_ivector */ /******************/ void free_imatrix(imatrix m) { free((int *) *m); free((int *) m); } /* free_imatrix */ /******************/ void free_icube(icube c) { free((int *) **c); free((int *) *c); free((int *) c); } /* free_icube */ /*************************************************** * memory allocate uli vectors, matrices, and cubes */ ulivector new_ulivector(int n) { ulivector v; v = (ulivector) calloc((size_t) n, sizeof(uli)); if (v == NULL) maerror("step 1 in new_ulivector"); return v; } /* new_ulivector */ /******************/ ulimatrix new_ulimatrix(int nrow, int ncol) { int i; ulimatrix m; m = (ulimatrix) calloc((size_t) nrow, sizeof(ulivector)); if (m == NULL) maerror("step 1 in new_ulimatrix"); *m = (ulivector) calloc((size_t) (nrow * ncol), sizeof(uli)); if (*m == NULL) maerror("step 2 in new_ulimatrix"); for (i = 1; i < nrow; i++) m[i] = m[i-1] + ncol; return m; } /* new_ulimatrix */ /******************/ ulicube new_ulicube(int ntri, int nrow, int ncol) { int i, j; ulicube c; c = (ulicube) calloc((size_t) ntri, sizeof(ulimatrix)); if (c == NULL) maerror("step 1 in new_ulicube"); *c = (ulimatrix) calloc((size_t) (ntri * nrow), sizeof(ulivector)); if (*c == NULL) maerror("step 2 in new_ulicube"); **c = (ulivector) calloc((size_t) (ntri * nrow * ncol), sizeof(uli)); if (**c == NULL) maerror("step 3 in new_ulicube"); for (j = 1; j < nrow; j++) c[0][j] = c[0][j-1] + ncol; for (i = 1; i < ntri; i++) { c[i] = c[i-1] + nrow; c[i][0] = c[i-1][0] + nrow * ncol; for (j = 1; j < nrow; j++) c[i][j] = c[i][j-1] + ncol; } return c; } /* new_ulicube */ /******************/ void free_ulivector(ulivector v) { free((uli *) v); } /* free_ulivector */ /******************/ void free_ulimatrix(ulimatrix m) { free((uli *) *m); free((uli *) m); } /* free_ulimatrix */ /******************/ void free_ulicube(ulicube c) { free((uli *) **c); free((uli *) *c); free((uli *) c); } /* free_ulicube */ /******************************************************************************/ /* check time */ /******************************************************************************/ #define TIMECHECK_INTERVALL 300 /* check timer and generate message roughly every TIMECHECK_INTERVALL seconds */ void checktime(time_t *starttime, /* starttime of overall part */ time_t *lasttime, /* lasttime of print out */ time_t *nowtime, /* current time (taken inside) */ uli done, /* number of tasks done */ uli sumtodo, /* sum of task todo */ int *mflag) /* LF needed to end line? */ { double tc2, mintogo, minutes, hours; /* check timer */ time(nowtime); if ( (*nowtime - *lasttime) > TIMECHECK_INTERVALL) { /* every TIMECHECK_INTERVAL seconds */ /* percentage of completed tasks */ if (*mflag == 0) { fprintf(STDOUT, "\n"); *mflag = 1; } tc2 = 100.0 * done/sumtodo; mintogo = (100.0-tc2) * (double) (*nowtime-*starttime)/60.0/tc2; hours = floor(mintogo/60.0); minutes = mintogo - 60.0*hours; fprintf(STDOUT, "%2.2f%%", tc2); fprintf(STDOUT, " completed (remaining"); fprintf(STDOUT, " time: %.0f", hours); fprintf(STDOUT, " hours %.0f", minutes); fprintf(STDOUT, " minutes)\n"); fflush(STDOUT); *lasttime = *nowtime; } /* else {fprintf(stdout,"t%ld,", *nowtime - *lasttime); fflush(stdout);} */ } /* checktime */ #ifndef SPRNG /******************************************************************************/ /* random numbers generator (Numerical recipes) */ /******************************************************************************/ /* variable */ long idum; /* definitions */ #define IM1 2147483563 #define IM2 2147483399 #define AM (1.0/IM1) #define IMM1 (IM1-1) #define IA1 40014 #define IA2 40692 #define IQ1 53668 #define IQ2 52774 #define IR1 12211 #define IR2 3791 #define NTAB 32 #define NDIV (1+IMM1/NTAB) #define EPS 1.2e-7 #define RNMX (1.0-EPS) double randomunitintervall() /* Long period (> 2e18) random number generator. Returns a uniform random deviate between 0.0 and 1.0 (exclusive of endpoint values). Source: Press et al., "Numerical recipes in C", Cambridge University Press, 1992 (chapter 7 "Random numbers", ran2 random number generator) */ { int j; long k; static long idum2=123456789; static long iy=0; static long iv[NTAB]; double temp; if (idum <= 0) { if (-(idum) < 1) idum=1; else idum=-(idum); idum2=(idum); for (j=NTAB+7;j>=0;j--) { k=(idum)/IQ1; idum=IA1*(idum-k*IQ1)-k*IR1; if (idum < 0) idum += IM1; if (j < NTAB) iv[j] = idum; } iy=iv[0]; } k=(idum)/IQ1; idum=IA1*(idum-k*IQ1)-k*IR1; if (idum < 0) idum += IM1; k=idum2/IQ2; idum2=IA2*(idum2-k*IQ2)-k*IR2; if (idum2 < 0) idum2 += IM2; j=iy/NDIV; iy=iv[j]-idum2; iv[j] = idum; if (iy < 1) iy += IMM1; if ((temp=AM*iy) > RNMX) return RNMX; else return temp; } /* randomunitintervall */ #undef IM1 #undef IM2 #undef AM #undef IMM1 #undef IA1 #undef IA2 #undef IQ1 #undef IQ2 #undef IR1 #undef IR2 #undef NTAB #undef NDIV #undef EPS #undef RNMX int initrandom(int seed) /* RAND4 */ { srand((unsigned) time(NULL)); if (seed < 0) seed = rand(); idum=-(long) seed; fflush(stderr); # ifndef PARALLEL fprintf(stderr,"Using RAND4 Random Number Generator\n"); # ifdef RANDVERBOSE1 fprintf(stderr, "!!! random seed set to %d !!!\n", seed); # endif /* RANDVERBOSE1 */ # else /* PARALLEL */ { int n; for (n=0; n t-s; i--) { /* random integer in the range [0, still to do = i-1] */ randidx = randominteger(i); /* integer from array of free ints to slist */ slist[t - i] = isfree[randidx]; /* reduce list by moving last free to last chosen */ isfree[randidx] = isfree[i-1]; } free_ivector(isfree); } /* chooser */ /******************/ /* Draw s numbers from the set 0,1,2,..,t-1 and put them into slist (every number can be drawn only one time) */ void fixedchooser(int t, int s, ivector slist) { int i; for (i = 0; i < s; i++) { /* random integer in the range [0, s-1] */ slist[i] = i; } } /* fixedchooser */ /******************************************************************************/ /* Saver variants of ANSI C routines */ /******************************************************************************/ /* a realloc function that works also on non-ANSI compilers */ void *myrealloc(void *p, size_t s) { if (p == NULL) return malloc(s); else return realloc(p, s); } /* myrealloc */ /******************/ /* safer variant of gets */ /* Reads characters from stdin until a newline character or EOF is received. The newline is not made part of the string. If an error occurs a null string \0 is returned */ cvector mygets() { int c, n; cvector str; str = new_cvector(100); n = 0; c = getchar(); while ((c != '\n') && (c != '\r') && (n < 99) && (c != EOF) && !ferror(stdin)) { str[n] = (char) c; c = getchar(); n++; } if (c == EOF || ferror(stdin)) { str[0] = '\0'; } else { str[n] = '\0'; } return str; } /* mygets */ /******************************************************************************/ /* minimization of a function by Brents method (Numerical Recipes) */ /******************************************************************************/ double brent(double, double, double, double (*f )(double ), double, double *, double *, double, double, double, int *); #define ITMAX 100 #define CGOLD 0.3819660 #define GOLD 1.618034 #define GLIMIT 100.0 #define TINY 1.0e-20 #define ZEPS 1.0e-10 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); #define SIGN(a,b) ((b) >= 0.0 ? fabs(a) : -fabs(a)) /* Brents method in one dimension */ double brent( double ax, /* three x-values ax < bx < cx */ double bx, /* or ax > bx > cx */ double cx, double (*f)(double), /* function to minimize, f(bx)=min(f(ax),f(bx),f(cx)) */ double tol, /* describes the precision */ double *foptx, double *f2optx, double fax, /* f(ax), already precomputed outside of brent() */ double fbx, /* f(bx), already precomputed outside of brent() */ double fcx, /* f(cx), already precomputed outside of brent() */ int *converged) /* not converged error flag */ { int iter; double a,b,d=0,etemp,fu,fv,fw,fx,p,q,r,tol1,tol2,u,v,w,x,xm; double xw,wv,vx; double e=0.0; *converged=TRUE; a=(ax < cx ? ax : cx); /* is the order correct? If not, exchange ax and cx */ b=(ax > cx ? ax : cx); x=bx; /* store 'middle' x, and y=fx */ fx=fbx; if (fax < fcx) { w=ax; fw=fax; v=cx; fv=fcx; } else { w=cx; fw=fcx; v=ax; fv=fax; } for (iter=1;iter<=ITMAX;iter++) { /* iteration loop */ xm=0.5*(a+b); tol2=2.0*(tol1=tol*fabs(x)+ZEPS); /* is precision OK? I.e., are a and b close enough. */ if (fabs(x-xm) <= (tol2-0.5*(b-a))) { /* yes -> finish */ *foptx = fx; /* return current f(x) */ if ((x==w) && (x==v)) { /* to avoid FPE errors by zero-division */ v=x-ZEPS; w=x+ZEPS; fv=(*f)(v); fw=(*f)(w); } xw = x-w; wv = w-v; vx = v-x; *f2optx = 2.0*(fv*xw + fx*wv + fw*vx)/ (v*v*xw + x*x*wv + w*w*vx); /* return S.E. of f(x) */ #if 0 fprintf(stderr, "XXXX: x=%f f(x)=%f=%f S.E.=%f w=%f v=%f\n", x, *foptx, fx, *f2optx, w, v); #endif return x; /* return minimum x-value */ } if (fabs(e) > tol1) { /* compute a parabolic fit */ r=(x-w)*(fx-fv); q=(x-v)*(fx-fw); p=(x-v)*q-(x-w)*r; q=2.0*(q-r); if (q > 0.0) p = -p; q=fabs(q); etemp=e; e=d; /* determine acceptability of the parabolic fit */ if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) /* compute golden section of the larger segment max(a-x,b-x) */ d=CGOLD*(e=(x >= xm ? a-x : b-x)); else { /* accept the parabolic step */ d=p/q; u=x+d; if (u-a < tol2 || b-u < tol2) d=SIGN(tol1,xm-x); } } else { /* compute golden section of the larger segment max(a-x,b-x) */ d=CGOLD*(e=(x >= xm ? a-x : b-x)); } u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); fu=(*f)(u); /* new u better than old x ? */ if (fu <= fx) { /* yes -> accept it */ if (u >= x) a=x; else b=x; SHFT(v,w,x,u) /* ...and use the new values */ SHFT(fv,fw,fx,fu) } else { if (u < x) a=u; else b=u; if (fu <= fw || w == x) { v=w; w=u; fv=fw; fw=fu; } else if (fu <= fv || v == x || v == w) { v=u; fv=fu; } } } /* end loop */ /* the function should never get here, i.e., the search did not converge within ITMAX iterations */ *converged=FALSE; *foptx = fx; /* return f(x) */ if ((x==w) && (x==v)) { /* regularize to avoid FPE errors by zero-division */ v=x-ZEPS; w=x+ZEPS; fv=(*f)(v); fw=(*f)(w); } xw = x-w; wv = w-v; vx = v-x; *f2optx = 2.0*(fv*xw + fx*wv + fw*vx)/ (v*v*xw + x*x*wv + w*w*vx); /* return S.E. of f(x) */ #if 0 fprintf(stderr, "YYYY: x=%f f(x)=%f=%f S.E.=%f w=%f v=%f\n", x, *foptx, fx, *f2optx, w, v); #endif return x; /* return minimum x-value */ } /* brent */ #undef ITMAX #undef CGOLD #undef ZEPS #undef SHFT #undef SIGN #undef GOLD #undef GLIMIT #undef TINY /******************/ /* one-dimensional minimization - as input a lower and an upper limit and a trial value for the minimum is needed: xmin < xguess < xmax the function and a fractional tolerance has to be specified onedimenmin returns the optimal x value and the value of the function and its second derivative at this point */ double onedimenmin( double xmin, double xguess, double xmax, double (*f)(double), double tol, double *fx, double *f2x) { double eps, optx, ax, bx, cx, fa, fb, fc; int converged; /* not converged error flag */ /* first attempt to bracketize minimum */ eps = xguess*tol*50.0; ax = xguess - eps; if (ax < xmin) ax = xmin; bx = xguess; cx = xguess + eps; if (cx > xmax) cx = xmax; /* check if this works */ fa = (*f)(ax); fb = (*f)(bx); fc = (*f)(cx); /* if it works use these borders else be conservative */ if ((fa < fb) || (fc < fb)) { if (ax != xmin) fa = (*f)(xmin); if (cx != xmax) fc = (*f)(xmax); optx = brent(xmin, xguess, xmax, f, tol, fx, f2x, fa, fb, fc, &converged); } else optx = brent(ax, bx, cx, f, tol, fx, f2x, fa, fb, fc, &converged); return optx; /* return optimal x */ } /* onedimenmin */ /******************/ /* two-dimensional minimization with borders and calculations of standard errors */ /* we optimize along basis vectors - not very optimal but it seems to work well */ void twodimenmin(double tol, int active1, double min1, double *x1, double max1, double (*func1)(double), double *err1, int active2, double min2, double *x2, double max2, double (*func2)(double), double *err2) { int it, nump, change; double x1old, x2old; double fx, f2x; it = 0; nump = 0; /* count number of parameters */ if (active1) nump++; if (active2) nump++; do { /* repeat until nothing changes any more */ it++; change = FALSE; /* optimize first variable */ if (active1) { if ((*x1) <= min1) (*x1) = min1 + 0.2*(max1-min1); if ((*x1) >= max1) (*x1) = max1 - 0.2*(max1-min1); x1old = (*x1); (*x1) = onedimenmin(min1, (*x1), max1, func1, tol, &fx, &f2x); if ((*x1) < min1) (*x1) = min1; if ((*x1) > max1) (*x1) = max1; /* same tolerance as 1D minimization */ if (fabs((*x1) - x1old) > 3.3*tol) change = TRUE; /* standard error */ f2x = fabs(f2x); if (1.0/(max1*max1) < f2x) (*err1) = sqrt(1.0/f2x); else (*err1) = max1; } /* optimize second variable */ if (active2) { if ((*x2) <= min2) (*x2) = min2 + 0.2*(max2-min2); if ((*x2) >= max2) (*x2) = max2 - 0.2*(max2-min2); x2old = (*x2); (*x2) = onedimenmin(min2, (*x2), max2, func2, tol, &fx, &f2x); if ((*x2) < min2) (*x2) = min2; if ((*x2) > max2) (*x2) = max2; /* same tolerance as 1D minimization */ if (fabs((*x2) - x2old) > 3.3*tol) change = TRUE; /* standard error */ f2x = fabs(f2x); if (1.0/(max2*max2) < f2x) (*err2) = sqrt(1.0/f2x); else (*err2) = max2; } if (nump == 1) return; } while (it != MAXITS && change); return; } /* twodimenmin */ tree-puzzle-5.2/src/util.h0000644000076400001440000000557010073365407011260 /* * util.h * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifndef _UTIL_ #define _UTIL_ #include #include #include #include /* * general definitions */ #define TRUE 1 #define FALSE 0 #ifdef PARALLEL extern long int PP_randn; extern long int PP_rand; #endif /* * type definitions */ typedef unsigned long int uli; typedef double *dvector, **dmatrix, ***dcube; typedef char *cvector, **cmatrix, ***ccube; typedef int *ivector, **imatrix, ***icube; typedef uli *ulivector, **ulimatrix, ***ulicube; /* * prototypes of functions defined in util.c */ void maerror(char *message); dvector new_dvector(int n); dmatrix new_dmatrix(int nrow, int ncol); dcube new_dcube(int ntri, int nrow, int ncol); void free_dvector(dvector v); void free_dmatrix(dmatrix m); void free_dcube(dcube c); cvector new_cvector(int n); cmatrix new_cmatrix(int nrow, int ncol); ccube new_ccube(int ntri, int nrow, int ncol); void free_cvector(cvector v); void free_cmatrix(cmatrix m); void free_ccube(ccube c); ivector new_ivector(int n); imatrix new_imatrix(int nrow, int ncol); icube new_icube(int ntri, int nrow, int ncol); void free_ivector(ivector v); void free_imatrix(imatrix m); void free_icube(icube c); ulivector new_ulivector(int n); ulimatrix new_ulimatrix(int nrow, int ncol); ulicube new_ulicube(int ntri, int nrow, int ncol); void free_ulivector(ulivector v); void free_ulimatrix(ulimatrix m); void free_ulicube(ulicube c); /* check timer and generate message roughly every 15 minutes */ void checktime(time_t *starttime, /* starttime of overall part */ time_t *lasttime, /* lasttime of print out */ time_t *nowtime, /* current time (taken inside) */ uli done, /* number of tasks done */ uli sumtodo, /* sum of task todo */ int *mflag); /* LF needed to end line? */ double randomunitintervall(void); int initrandom(int seed); int randominteger(int n); void chooser(int t, int s, ivector slist); void fixedchooser(int t, int s, ivector slist); void *myrealloc(void *, size_t); cvector mygets(void); #define MAXITS 10 /* maximum number of iterations in twoedimenmin */ double onedimenmin(double, double, double, double (*f )(double ), double, double *, double *); void twodimenmin(double, int, double, double *, double, double (*func1 )(double ), double *, int, double, double *, double, double (*func2 )(double ), double *); #endif tree-puzzle-5.2/src/ppuzzle.c0000644000076400001440000023345610073365412012011 /* * ppuzzle.c * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifdef HAVE_CONFIG_H # include #endif #define EXTERN extern #include #include #include "ppuzzle.h" int PP_IamMaster; int PP_IamSlave; int PP_Myid; int PP_MyMaster; int PP_NumProcs; MPI_Comm PP_Comm; int *freeslaves; /* Queue of free slaves */ int firstslave, /* headpointer of queue */ lastslave; /* tailpointer of queue */ int *permutsent, *permutrecved, *quartsent, *quartrecved, *doquartsent, *doquartrecved, *splitsent, *splitrecved, *permutsentn, *permutrecvedn, *quartsentn, *quartrecvedn, *doquartsentn, *doquartrecvedn, *splitsentn, *splitrecvedn; double *walltimes, *cputimes; double *fullwalltimes, *fullcputimes; double *altwalltimes, *altcputimes; int PP_permutsent = 0; /* # of */ int PP_permutrecved = 0; /* # of */ int PP_quartsent = 0; /* # of */ int PP_quartrecved = 0; /* # of */ int PP_doquartsent = 0; /* # of */ int PP_doquartrecved = 0; /* # of */ int PP_splitsent = 0; /* # of */ int PP_splitrecved = 0; /* # of */ int PP_permutsentn = 0; /* # of */ int PP_permutrecvedn = 0; /* # of */ int PP_quartsentn = 0; /* # of */ int PP_quartrecvedn = 0; /* # of */ int PP_doquartsentn = 0; /* # of */ int PP_doquartrecvedn = 0; /* # of */ int PP_splitsentn = 0; /* # of */ int PP_splitrecvedn = 0; /* # of */ double PP_starttime = 0, PP_stoptime = 0, PP_inittime = 0, PP_paramcomptime = 0, PP_paramsendtime = 0, PP_quartcomptime = 0, PP_quartsendtime = 0, PP_puzzletime = 0, PP_treetime = 0, PP_lasttime = 0; int PP_MaxSlave = 0; /********************************************************************* * debugging * *********************************************************************/ static int deb_num = 0; void fprintfdebug(FILE *fp, char s[], char f[], int l) { fprintf(fp, "[%2d] %s (%s:%d)\n", deb_num++, s, f, l); } /* fprintfdebug(stderr, "debug message", __FILE__, __LINE__); */ /********************************************************************* * miscellaneous utilities * *********************************************************************/ int dcmp(const void *a, const void *b) { if (*(double *)a > *(double *)b) return (-1); else if (*(double *)a < *(double *)b) return 1; else return 0; } /* dcmp */ /******************/ void PP_cmpd(int rank, double a, double b) { if (a != b) fprintf(STDOUT, "(%2d) *** %.3f != %.3f\n", rank, a, b); } /* PP_cmpd */ /******************/ void PP_cmpi(int rank, int a, int b) { if (a != b) fprintf(STDOUT, "(%2d) *** %d != %d\n", rank, a, b); } /* PP_cmpi */ /******************/ double PP_timer() { double tmptime; if (PP_lasttime == 0) { PP_lasttime = MPI_Wtime(); return(0); } else { tmptime = PP_lasttime; PP_lasttime = MPI_Wtime(); return(PP_lasttime - tmptime); } } /* PP_timer */ /******************/ void PP_Printerror(FILE *of, int id, int err) { char errstr[MPI_MAX_ERROR_STRING]; int errstrlen; if ((err > MPI_SUCCESS) && (err <= MPI_ERR_LASTCODE)) { MPI_Error_string(err, errstr, &errstrlen); fprintf(of, "(%2d) MPI ERROR %d : %s\n", id, err, errstr); } else { if (err == MPI_SUCCESS) fprintf(of, "(%2d) MPI ERROR %d : No error\n", id, err); else fprintf(of, "(%2d) MPI ERROR %d : unknown error number\n", id, err); } } /* PP_Printerror */ /******************/ void PP_Printbiparts(cmatrix biparts) { int n1, n2; for (n1=0; n1<(Maxspc-3); n1++) { if (n1==0) fprintf(STDOUT, "(%2d) bipartition : ", PP_Myid); else fprintf(STDOUT, "(%2d) : ", PP_Myid); for (n2=0; n20)&&(lx (Maxspc - 1)) { chunk -= Maxspc - ly - 1; lx ++; ly = lx; } else { ly += chunk; chunk = 0; } } *x = lx; *y = ly; return; } void PP_NextCoord_atamt(int* x, int* y, int chunk, int dimen) { int lx = *x, ly = *y; while ((chunk>0)&&(lx lx) { chunk -= lx - ly + 1; lx ++; ly = 0; } else { ly += chunk; chunk = 0; } } *x = lx; *y = ly; return; } void PP_VectorToDM(int x, int y, int chunk, double* result) { int i; for (i=0; i %ld\n", PP_Myid, e, f, g, h, quart2num(e, f, g, h)); # endif /* PVERBOSE3 */ badqs++; badtaxon[e]++; badtaxon[f]++; badtaxon[g]++; badtaxon[h]++; } /* if badquartet */ return(qpbranching); } /* PP_do_write_quart */ /********************************************************************* * sending/receiving the important sizes and parameter (M->S) * *********************************************************************/ #ifndef USE_WINDOWS void PP_SendSizes(int mspc, int msite, int ncats, int nptrn, int rad, int outgr, double frconst, int rseed, int fixedorder, int consensus) #else void PP_SendSizes(int mspc, int msite, int alimsite, int alistart, int aliend, int ncats, int nptrn, int rad, int outgr, double frconst, int rseed, int fixedorder, int consensus) #endif { #ifndef USE_WINDOWS # define NUMINT 9 # define NUMDBL 1 #else # define NUMINT 12 # define NUMDBL 1 #endif int ints[NUMINT]; double doubles[NUMDBL]; MPI_Datatype Dtypes[2] = {MPI_INT, MPI_DOUBLE}; int Dtypelens[2] = {NUMINT , NUMDBL}; MPI_Aint Dtypeaddr[2]; MPI_Datatype PP_Sizes; int dest; int error; # ifdef PVERBOSE2 fprintf(STDOUT, "(%2d) Sending: Maxspc=%d Maxsite=%d numcats=%d\n", PP_Myid, mspc, msite, ncats); fprintf(STDOUT, "(%2d) Numprtn=%d tpmradix=%d fracconst=%.3f\n", PP_Myid, nptrn, rad, frconst); # endif /* PVERBOSE2 */ ints[0] = mspc; ints[1] = msite; ints[2] = ncats; ints[3] = nptrn; ints[4] = rad; ints[5] = outgr; ints[6] = rseed; ints[7] = fixedorder; ints[8] = consensus; #ifdef USE_WINDOWS ints[9] = alimsite; ints[10] = alistart; ints[11] = aliend; #endif doubles[0] = frconst; MPI_Address(ints, Dtypeaddr); MPI_Address(doubles, (Dtypeaddr+1)); MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Sizes); MPI_Type_commit(&PP_Sizes); for (dest=1; dest (%2d) Sent Sizes\n", PP_Myid, dest); # endif /* PVERBOSE3 */ } /* for each slave */ MPI_Type_free(&PP_Sizes); # ifdef PVERBOSE3 fprintf(STDOUT, "(%2d) ... Sent Sizes\n", PP_Myid); # endif /* PVERBOSE3 */ # undef NUMINT # undef NUMDBL } /* PP_SendSizes */ /******************/ #ifndef USE_WINDOWS void PP_RecvSizes(int *mspc, int *msite, int *ncats, int *nptrn, int *rad, int *outgr, double *frconst, int *rseed, int *fixedorder, int *consensus) #else void PP_RecvSizes(int *mspc, int *msite, int *alimsite, int *alistart, int *aliend, int *ncats, int *nptrn, int *rad, int *outgr, double *frconst, int *rseed, int *fixedorder, int *consensus) #endif { #ifndef USE_WINDOWS # define NUMINT 9 # define NUMDBL 1 #else # define NUMINT 12 # define NUMDBL 1 #endif int ints[NUMINT]; double doubles[NUMDBL]; MPI_Datatype Dtypes[2] = {MPI_INT, MPI_DOUBLE}; int Dtypelens[2] = {NUMINT , NUMDBL}; MPI_Aint Dtypeaddr[2]; MPI_Datatype PP_Sizes; MPI_Status stat; int error; # ifdef PVERBOSE3 fprintf(STDOUT, "(%2d) Receiving Sizes ...\n", PP_Myid); # endif /* PVERBOSE3 */ MPI_Address(ints, Dtypeaddr); MPI_Address(doubles, (Dtypeaddr+1)); MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Sizes); MPI_Type_commit(&PP_Sizes); error = MPI_Probe(PP_MyMaster, MPI_ANY_TAG, PP_Comm, &stat); if (error != MPI_SUCCESS) PP_Printerror(STDOUT, 700+PP_Myid, error); if (stat.MPI_TAG != PP_SIZES) { if (stat.MPI_TAG == PP_DONE) { PP_RecvDone(); # ifdef PVERBOSE1 fprintf(STDOUT, "(%2d) Finishing...\n", PP_Myid); # endif /* PVERBOSE1 */ MPI_Finalize(); exit(1); } else { fprintf(STDOUT, "(%2d) Error: unexpected TAG received...\n", PP_Myid); MPI_Finalize(); exit(1); } } error = MPI_Recv(MPI_BOTTOM, 1, PP_Sizes, PP_MyMaster, MPI_ANY_TAG, PP_Comm, &stat); if (error != MPI_SUCCESS) PP_Printerror(STDOUT, 700+PP_Myid, error); if (stat.MPI_TAG != PP_SIZES) { fprintf(STDOUT, "(%2d) Error: unexpected TAG received...\n", PP_Myid); MPI_Finalize(); exit(1); } *mspc = ints[0]; *msite = ints[1]; *ncats = ints[2]; *nptrn = ints[3]; *rad = ints[4]; *outgr = ints[5]; *rseed = ints[6]; *fixedorder = ints[7]; *consensus = ints[8]; #ifdef USE_WINDOWS *alimsite = ints[9]; *alistart = ints[10]; *aliend = ints[11]; #endif *frconst = doubles[0]; MPI_Type_free(&PP_Sizes); # ifdef PVERBOSE2 fprintf(STDOUT, "(%2d) <- (%2d) Received: Maxspec=%d Maxsite=%d numcats=%d\n", PP_Myid, PP_MyMaster, *mspc, *msite, *ncats); fprintf(STDOUT, "(%2d) Numprtn=%d tpmradix=%d fracconst=%.3f\n", PP_Myid, *nptrn, *rad, *frconst); # endif /* PVERBOSE2 */ # undef NUMINT # undef NUMDBL } /* PP_RecvSizes */ /********************************************************************* * sending/receiving the data matrizes (M->S) * *********************************************************************/ void PP_RecvData( cmatrix Seqpat, /* cmatrix (Maxspc x Numptrn) */ ivector Alias, /* ivector (Maxsite) */ ivector Weight, /* ivector (Numptrn) */ ivector constpat, dvector Rates, /* dvector (numcats) */ dvector Eval, /* dvector (tpmradix) */ dvector Freqtpm, dmatrix Evec, /* dmatrix (tpmradix x tpmradix) */ dmatrix Ievc, dmatrix iexp, /* dmatrix Distanmat,*/ /*epe*/ /* dmatrix (Maxspc x Maxspc) */ dcube ltprobr) /* dcube (numcats x tpmradix x tpmradix) */ { MPI_Datatype Dtypes[12]; int Dtypelens[12]; MPI_Aint Dtypeaddr[12]; MPI_Datatype PP_Data; MPI_Status stat; int error; # ifdef PVERBOSE3 fprintf(STDOUT, "(%2d) Receiving Sizes ...\n", PP_Myid); # endif /* PVERBOSE2 */ Dtypes [0] = MPI_CHAR; Dtypelens [0] = Maxspc * Numptrn; MPI_Address(&(Seqpat[0][0]), &(Dtypeaddr[0])); Dtypes [1] = MPI_INT; Dtypelens [1] = Maxsite ; MPI_Address(&(Alias[0]), &(Dtypeaddr[1])); Dtypes [2] = MPI_INT; Dtypelens [2] = Numptrn ; MPI_Address(&(Weight[0]), &(Dtypeaddr[2])); Dtypes [3] = MPI_INT; Dtypelens [3] = Numptrn ; MPI_Address(&(constpat[0]), &(Dtypeaddr[3])); Dtypes [4] = MPI_DOUBLE; Dtypelens [4] = numcats ; MPI_Address(&(Rates[0]), &(Dtypeaddr[4])); Dtypes [5] = MPI_DOUBLE; Dtypelens [5] = tpmradix ; MPI_Address(&(Eval[0]), &(Dtypeaddr[5])); Dtypes [6] = MPI_DOUBLE; Dtypelens [6] = tpmradix ; MPI_Address(&(Freqtpm[0]), &(Dtypeaddr[6])); Dtypes [7] = MPI_DOUBLE; Dtypelens [7] = tpmradix * tpmradix ; MPI_Address(&(Evec[0][0]), &(Dtypeaddr[7])); Dtypes [8] = MPI_DOUBLE; Dtypelens [8] = tpmradix * tpmradix ; MPI_Address(&(Ievc[0][0]), &(Dtypeaddr[8])); Dtypes [9] = MPI_DOUBLE; Dtypelens [9] = tpmradix * tpmradix ; MPI_Address(&(iexp[0][0]), &(Dtypeaddr[9])); Dtypes [10] = MPI_DOUBLE; Dtypelens [10] = Maxspc * Maxspc ; MPI_Address(&(Distanmat[0][0]), &(Dtypeaddr[10])); Dtypes [11] = MPI_DOUBLE; Dtypelens [11] = numcats * tpmradix * tpmradix ; MPI_Address(&(ltprobr[0][0][0]), &(Dtypeaddr[11])); MPI_Type_struct(12, Dtypelens, Dtypeaddr, Dtypes, &PP_Data); MPI_Type_commit(&PP_Data); error = MPI_Probe(PP_MyMaster, MPI_ANY_TAG, PP_Comm, &stat); if (error != MPI_SUCCESS) PP_Printerror(STDOUT, 700+PP_Myid, error); if (stat.MPI_TAG != PP_DATA) { if (stat.MPI_TAG == PP_DONE) { PP_RecvDone(); # ifdef PVERBOSE1 fprintf(STDOUT, "(%2d) Finishing...\n", PP_Myid); # endif /* PVERBOSE1 */ MPI_Finalize(); exit(1); } else { fprintf(STDOUT, "(%2d) Error: unexpected TAG received...\n", PP_Myid); MPI_Finalize(); exit(1); } } error = MPI_Recv(MPI_BOTTOM, 1, PP_Data, PP_MyMaster, PP_DATA, PP_Comm, &stat); if (error != MPI_SUCCESS) PP_Printerror(STDOUT, 900+PP_Myid, error); # ifdef PVERBOSE2 fprintf(STDOUT, "(%2d) <- (%2d) Received : Alias(0)=%d - Weight(0)=%d - constpat(0)=%d\n", PP_Myid, PP_MyMaster, Alias[0], Weight[0], constpat[0]); fprintf(STDOUT, "(%2d) Rates(0)=%.3f - Eval(0)=%.3f - Freqtpm(0)=%.3f\n", PP_Myid, Rates[0], Eval[0], Freqtpm[0]); fprintf(STDOUT, "(%2d) Evec(0,0)=%.3f - Ievc(0,0)=%.3f - iexp(0,0)=%.3f - Distanmat(0,1)=%.3f\n", PP_Myid, Evec[0][0], Ievc[0][0], iexp[0][0], Distanmat[0][1]); fprintf(STDOUT, "(%2d) Distanmat(0,1)=%.3f\n", PP_Myid, Distanmat[0][1]); fprintf(STDOUT, "(%2d) ltprobr(0,0,0)=%.3f\n", PP_Myid, ltprobr[0][0][0]); # endif /* PVERBOSE2 */ MPI_Type_free(&PP_Data); } /* PP_RecvData */ /******************/ void PP_SendData( cmatrix Seqpat, /* cmatrix (Maxspc x Numptrn) */ ivector Alias, /* ivector (Maxsite) */ ivector Weight, /* ivector (Numptrn) */ ivector constpat, dvector Rates, /* dvector (numcats) */ dvector Eval, /* dvector (tpmradix) */ dvector Freqtpm, dmatrix Evec, /* dmatrix (tpmradix x tpmradix) */ dmatrix Ievc, dmatrix iexp, /* dmatrix Distanmat,*/ /*epe*/ /* dmatrix (Maxspc x Maxspc) */ dcube ltprobr) /* dcube (numcats x tpmradix x tpmradix) */ { MPI_Datatype Dtypes[12]; int Dtypelens[12]; MPI_Aint Dtypeaddr[12]; MPI_Datatype PP_Data; int dest; int error; # ifdef PVERBOSE2 fprintf(STDOUT, "(%2d) Sending: Alias(0)=%d - Weight(0)=%d - constpat(0)=%d\n", PP_Myid, Alias[0], Weight[0], constpat[0]); fprintf(STDOUT, "(%2d) Rates(0)=%.3f - Eval(0)=%.3f - Freqtpm(0)=%.3f\n", PP_Myid, Rates[0], Eval[0], Freqtpm[0]); fprintf(STDOUT, "(%2d) Evec(0,0)=%.3f - Ievc(0,0)=%.3f - iexp(0,0)=%.3f - Distanmat(0,1)=%.3f\n", PP_Myid, Evec[0][0], Ievc[0][0], iexp[0][0], Distanmat[0][1]); fprintf(STDOUT, "(%2d) ltprobr(0,0,0)=%.3f\n", PP_Myid, ltprobr[0][0][0]); # endif /* PVERBOSE2 */ Dtypes [0] = MPI_CHAR; Dtypelens [0] = Maxspc * Numptrn; MPI_Address(&(Seqpat[0][0]), &(Dtypeaddr[0])); Dtypes [1] = MPI_INT; Dtypelens [1] = Maxsite ; MPI_Address(&(Alias[0]), &(Dtypeaddr[1])); Dtypes [2] = MPI_INT; Dtypelens [2] = Numptrn ; MPI_Address(&(Weight[0]), &(Dtypeaddr[2])); Dtypes [3] = MPI_INT; Dtypelens [3] = Numptrn ; MPI_Address(&(constpat[0]), &(Dtypeaddr[3])); Dtypes [4] = MPI_DOUBLE; Dtypelens [4] = numcats ; MPI_Address(&(Rates[0]), &(Dtypeaddr[4])); Dtypes [5] = MPI_DOUBLE; Dtypelens [5] = tpmradix ; MPI_Address(&(Eval[0]), &(Dtypeaddr[5])); Dtypes [6] = MPI_DOUBLE; Dtypelens [6] = tpmradix ; MPI_Address(&(Freqtpm[0]), &(Dtypeaddr[6])); Dtypes [7] = MPI_DOUBLE; Dtypelens [7] = tpmradix * tpmradix ; MPI_Address(&(Evec[0][0]), &(Dtypeaddr[7])); Dtypes [8] = MPI_DOUBLE; Dtypelens [8] = tpmradix * tpmradix ; MPI_Address(&(Ievc[0][0]), &(Dtypeaddr[8])); Dtypes [9] = MPI_DOUBLE; Dtypelens [9] = tpmradix * tpmradix ; MPI_Address(&(iexp[0][0]), &(Dtypeaddr [9])); Dtypes [10] = MPI_DOUBLE; Dtypelens [10] = Maxspc * Maxspc ; MPI_Address(&(Distanmat[0][0]), &(Dtypeaddr[10])); Dtypes [11] = MPI_DOUBLE; Dtypelens [11] = numcats * tpmradix * tpmradix ; MPI_Address(&(ltprobr[0][0][0]), &(Dtypeaddr[11])); MPI_Type_struct(12, Dtypelens, Dtypeaddr, Dtypes, &PP_Data); MPI_Type_commit(&PP_Data); for (dest=1; dest (%2d) Sent Data\n", PP_Myid, dest); # endif /* PVERBOSE2 */ } /* for each slave */ MPI_Type_free(&PP_Data); # ifdef PVERBOSE3 fprintf(STDOUT, "(%2d) ... Sent Data\n", PP_Myid); # endif /* PVERBOSE2 */ } /* PP_SendData */ /************************************************************************** * procedures to send the request to compute a single quartet (M->S) * **************************************************************************/ void PP_SendDoQuart(int dest, int a, int b, int c, int d, int usebestq, int approx) { # define NUMINT 6 int ints[NUMINT]; int error; ints[0] = a; ints[1] = b; ints[2] = c; ints[3] = d; ints[4] = usebestq; ints[5] = approx; PP_doquartsent++; PP_doquartsentn++; # ifdef PVERBOSE2 fprintf(STDOUT, "(%2d) Sending -> (%2d): Quart(%d,%d,%d,%d)\n", PP_Myid, dest, a, b, c, d); # endif /* PVERBOSE2 */ error = MPI_Ssend(ints, NUMINT, MPI_INT, dest, PP_DOQUART, PP_Comm); if (error != MPI_SUCCESS) PP_Printerror(STDOUT, PP_Myid, error); # ifdef PVERBOSE3 fprintf(STDOUT, "(%2d) ... Sent \n", PP_Myid); # endif /* PVERBOSE3 */ # undef NUMINT } /* PP_SendDoQuart */ /******************/ void PP_RecvDoQuart(int *a, int *b, int *c, int *d, int *usebestq, int *approx) { # define NUMINT 6 int ints[NUMINT]; int error; MPI_Status stat; PP_doquartrecved++; PP_doquartrecvedn++; # ifdef PVERBOSE3 fprintf(STDOUT, "(%2d) Receiving: Quart\n", PP_Myid); # endif /* PVERBOSE3 */ error = MPI_Recv(ints, NUMINT, MPI_INT, PP_MyMaster, PP_DOQUART, PP_Comm, &stat); if (error != MPI_SUCCESS) PP_Printerror(STDOUT, 200+PP_Myid, error); *a = ints[0]; *b = ints[1]; *c = ints[2]; *d = ints[3]; *usebestq = ints[4]; *approx = ints[5]; # ifdef PVERBOSE2 fprintf(STDOUT, "(%2d) Received: Quart(%d,%d,%d,%d,%c)\n", PP_Myid, *a, *b, *c, *d, (approx ? 'A' : 'E')); # endif /* PVERBOSE2 */ # undef NUMINT } /* PP_RecvDoQuart */ /************************************************************************** * procedures to send the result of a single quartet (S->M) * **************************************************************************/ void PP_SendQuart(int a, int b, int c, int d, double d1, double d2, double d3, int usebestq, int approx) { # define NUMINT 6 # define NUMDBL 3 int ints[NUMINT]; double doubles[NUMDBL]; MPI_Datatype Dtypes[2] = {MPI_INT, MPI_DOUBLE}; int Dtypelens[2] = {NUMINT , NUMDBL}; MPI_Aint Dtypeaddr[2]; MPI_Datatype PP_Quart; int error; PP_quartsent++; PP_quartsentn++; ints[0] = a; ints[1] = b; ints[2] = c; ints[3] = d; doubles[0] = d1; doubles[1] = d2; doubles[2] = d3; ints[4] = usebestq; ints[5] = approx; MPI_Address(ints, Dtypeaddr); MPI_Address(doubles, (Dtypeaddr+1)); MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Quart); MPI_Type_commit(&PP_Quart); # ifdef PVERBOSE2 fprintf(STDOUT, "(%2d) Sending: Quart(%d,%d,%d,%d) = (%.3f, %.3f, %.3f)\n", PP_Myid, a, b, c, d, d1, d2, d3); # endif /* PVERBOSE2 */ error = MPI_Ssend(MPI_BOTTOM, 1, PP_Quart, PP_MyMaster, PP_QUART, PP_Comm); if (error != MPI_SUCCESS) PP_Printerror(STDOUT, 400+PP_Myid, error); MPI_Type_free(&PP_Quart); # ifdef PVERBOSE3 fprintf(STDOUT, "(%2d) ... Sent \n", PP_Myid); # endif /* PVERBOSE3 */ # undef NUMINT # undef NUMDBL } /* PP_SendQuart */ /******************/ void PP_RecvQuart(int *a, int *b, int *c, int *d, double *d1, double *d2, double *d3, int *usebestq, int *approx) { # define NUMINT 6 # define NUMDBL 3 int ints[NUMINT]; double doubles[NUMDBL]; MPI_Datatype Dtypes[2] = {MPI_INT, MPI_DOUBLE}; int Dtypelens[2] = {NUMINT , NUMDBL}; MPI_Aint Dtypeaddr[2]; MPI_Datatype PP_Quart; int error; MPI_Status stat; PP_quartrecved++; PP_quartrecvedn++; MPI_Address(ints, Dtypeaddr); MPI_Address(doubles, (Dtypeaddr+1)); MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_Quart); MPI_Type_commit(&PP_Quart); error = MPI_Recv(MPI_BOTTOM, 1, PP_Quart, MPI_ANY_SOURCE, PP_QUART, PP_Comm, &stat); if (error != MPI_SUCCESS) PP_Printerror(STDOUT, 500+PP_Myid, error); PP_putslave(stat.MPI_SOURCE); *a = ints[0]; *b = ints[1]; *c = ints[2]; *d = ints[3]; *d1 = doubles[0]; *d2 = doubles[1]; *d3 = doubles[2]; *usebestq = ints[4]; *approx = ints[5]; MPI_Type_free(&PP_Quart); # ifdef PVERBOSE2 fprintf(STDOUT, "(%2d) Received <- (%2d): Quart(%d,%d,%d,%d)=(%.3f, %.3f, %.3f)\n", PP_Myid, stat.MPI_SOURCE, *a, *b, *c, *d, *d1, *d2, *d3); # endif /* PVERBOSE2 */ # undef NUMINT # undef NUMDBL } /* PP_RecvQuart */ /************************************************************************** * procedures to send the request to compute a block of quartets (M->S) * **************************************************************************/ void PP_SendDoQuartBlock(int dest, uli firstq, uli amount, int usebestq, int approx) { # define NUMULI 4 uli ulongs[NUMULI]; int error; PP_doquartsent += amount; PP_doquartsentn++; # ifdef PVERBOSE2 fprintf(STDOUT, "(%2d) Sending: DOQuartBlock Signal\n", PP_Myid); # endif /* PVERBOSE2 */ ulongs[0] = firstq; ulongs[1] = amount; ulongs[2] = (uli)usebestq; ulongs[3] = (uli)approx; error = MPI_Ssend(ulongs, NUMULI, MPI_UNSIGNED_LONG, dest, PP_DOQUARTBLOCK, PP_Comm); if (error != MPI_SUCCESS) PP_Printerror(STDOUT, 2100+PP_Myid, error); # ifdef PVERBOSE3 fprintf(STDOUT, "(%2d) ... Sent DOQuartBlock Signal (addr:%ld, num:%ld)\n", PP_Myid, firstq, amount); # endif /* PVERBOSE3 */ # undef NUMULI } /* PP_SendDoQuartBlock */ /******************/ void PP_RecvDoQuartBlock(uli *firstq, uli *amount, uli **bq, int *usebestq, int *approx) { # define NUMULI 4 uli ulongs[NUMULI]; MPI_Status stat; int error; # ifdef PVERBOSE2 fprintf(STDOUT, "(%2d) Receiving: DOQuartBlock Signal\n", PP_Myid); # endif /* PVERBOSE2 */ error = MPI_Recv(&ulongs, NUMULI, MPI_UNSIGNED_LONG, PP_MyMaster, PP_DOQUARTBLOCK, PP_Comm, &stat); if (error != MPI_SUCCESS) PP_Printerror(STDOUT, 2100+PP_Myid, error); *firstq = ulongs[0]; *amount = ulongs[1]; *usebestq = (int)ulongs[2]; *approx = (int)ulongs[3]; *bq = calloc((size_t)*amount, sizeof(uli)); PP_doquartrecved += *amount; PP_doquartrecvedn++; # ifdef PVERBOSE3 fprintf(STDOUT, "(%2d) ... DOQuartBlock (addr:%ld, num:%ld)\n", PP_Myid, *firstq, *amount); # endif /* PVERBOSE3 */ # undef NUMULI } /* PP_RecvDoQuartBlock */ /********************************************************************* * procedures to send the results of a block of quartets (S->M) * *********************************************************************/ void PP_SendQuartBlock(uli startq, uli numofq, unsigned char *quartetinfo, uli fullresqs, /* number of fully resolved quartets */ uli partresqs, /* number of partly resolved quartets */ uli unresqs, /* number of unresolved quartets */ uli missingqs, /* number of missing quartets */ uli numofbq, uli *bq, int usebestq, int approx) { # define NUMULI 7 # define NUMINT 2 unsigned char *trueaddr; uli truenum; int error; int ints[NUMINT]; uli ulis[NUMULI]; MPI_Datatype Dtypes[2] = {MPI_UNSIGNED_LONG, MPI_INT}; int Dtypelens[2] = {NUMULI, NUMINT}; MPI_Aint Dtypeaddr[2]; MPI_Datatype PP_QBlockSpecs; MPI_Datatype DtypesRes[2] = {MPI_UNSIGNED_CHAR, MPI_UNSIGNED_LONG}; int DtypelensRes[2]; MPI_Aint DtypeaddrRes[2]; MPI_Datatype PP_QBlockRes; /* uli *bq; uli numofbq; */ PP_quartsent += numofq; PP_quartsentn++; truenum = (uli)((numofq+1)/2); trueaddr = (unsigned char *)(quartetinfo + (uli)(startq/2)); # ifdef PVERBOSE2 fprintf(STDOUT, "(%2d) Sending: startq=%lud numofq=%lud\n", PP_Myid, startq, numofq); fprintf(STDOUT, "(%2d) approx=%c\n", PP_Myid, (approx ? 'A' : 'E')); # endif /* PVERBOSE2 */ ints[0] = usebestq; ints[1] = approx; ulis[0] = startq; ulis[1] = numofq; ulis[2] = numofbq; ulis[3] = unresqs; /* number of unresolved quartets */ ulis[4] = partresqs; /* number of partly resolved quartets */ ulis[5] = fullresqs; /* number of fully resolved quartets */ ulis[6] = missingqs; /* number of missing quartets */ MPI_Address(ulis, Dtypeaddr); MPI_Address(ints, (Dtypeaddr+1)); MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_QBlockSpecs); MPI_Type_commit(&PP_QBlockSpecs); # ifdef PVERBOSE2 fprintf(STDOUT, "(%2d) Sending: xxPP_QuartBlockSpecs(0,%lu)=%d,%d\n", PP_Myid, truenum-1, trueaddr[0], trueaddr[truenum-1]); # endif /* PVERBOSE2 */ error = MPI_Ssend(MPI_BOTTOM, 1, PP_QBlockSpecs, PP_MyMaster, PP_QUARTBLOCKSPECS, PP_Comm); # ifdef PVERBOSE3 fprintf(STDOUT, "(%2d) ... Sent QuartBlockSpecs (%ld, %ld, %ld, %d)\n", PP_Myid, ulis[0], ulis[1], ulis[2], ints[0]); # endif /* PVERBOSE3 */ MPI_Address(trueaddr, DtypeaddrRes); DtypelensRes[0] = truenum; MPI_Address(bq, (DtypeaddrRes + 1)); DtypelensRes[1] = numofbq; MPI_Type_struct(2, DtypelensRes, DtypeaddrRes, DtypesRes, &PP_QBlockRes); MPI_Type_commit(&PP_QBlockRes); error = MPI_Ssend(MPI_BOTTOM, 1, PP_QBlockRes, PP_MyMaster, PP_QUARTBLOCK, PP_Comm); if (error != MPI_SUCCESS) PP_Printerror(STDOUT, PP_Myid, error); MPI_Type_free(&PP_QBlockSpecs); MPI_Type_free(&PP_QBlockRes); # ifdef PVERBOSE3 fprintf(STDOUT, "(%2d) ... Sent xxPP_QuartBlock(0,%lu)=%d,%d\n", PP_Myid, truenum-1, trueaddr[0], trueaddr[truenum-1]); # endif /* PVERBOSE3 */ # undef NUMULI # undef NUMINT } /* PP_SendQuartBlock */ /******************/ void PP_RecvQuartBlock(int slave, uli *startq, uli *numofq, unsigned char *quartetinfo, uli *fullresqs, /* number of fully resolved quartets */ uli *partresqs, /* number of partly resolved quartets */ uli *unresqs, /* number of unresolved quartets */ uli *missingqs, /* number of missing quartets */ int *usebestq, int *approx) { # define NUMULI 7 # define NUMINT 2 unsigned char *trueaddr; uli truenum; int error; int dest; int ints[NUMINT]; uli ulis[NUMULI]; MPI_Datatype Dtypes[2] = {MPI_UNSIGNED_LONG, MPI_INT}; int Dtypelens[2] = {NUMULI, NUMINT}; MPI_Aint Dtypeaddr[2]; MPI_Datatype PP_QBlockSpecs; MPI_Datatype DtypesRes[2] = {MPI_UNSIGNED_CHAR, MPI_UNSIGNED_LONG}; int DtypelensRes[2]; MPI_Aint DtypeaddrRes[2]; MPI_Datatype PP_QBlockRes; MPI_Status stat; uli count; uli idx; uli qstart; uli qend; int a, b, c, i; unsigned char quartettype; uli tmpunresqs = 0; /* number of unresolved quartets */ uli tmppartresqs = 0; /* number of partly resolved quartets */ uli tmpfullresqs = 0; /* number of fully resolved quartets */ uli tmpmissingqs = 0; /* number of missing quartets */ uli num; uli *numofbq; uli *bq; numofbq=# # ifdef PVERBOSE3 fprintf(STDOUT, "(%2d) Receiving QuartBlock ...\n", PP_Myid); # endif /* PVERBOSE3 */ MPI_Address(ulis, Dtypeaddr); MPI_Address(ints, (Dtypeaddr+1)); MPI_Type_struct(2, Dtypelens, Dtypeaddr, Dtypes, &PP_QBlockSpecs); MPI_Type_commit(&PP_QBlockSpecs); MPI_Probe(MPI_ANY_SOURCE, PP_QUARTBLOCKSPECS, PP_Comm, &stat); dest = stat.MPI_SOURCE; error = MPI_Recv(MPI_BOTTOM, 1, PP_QBlockSpecs, dest, PP_QUARTBLOCKSPECS, PP_Comm, &stat); if (error != MPI_SUCCESS) PP_Printerror(STDOUT, PP_Myid, error); *usebestq = ints[0]; *approx = ints[1]; *startq = ulis[0]; *numofq = ulis[1]; *numofbq = ulis[2]; *unresqs = ulis[3]; /* number of unresolved quartets */ *partresqs = ulis[4]; /* number of partly resolved quartets */ *fullresqs = ulis[5]; /* number of fully resolved quartets */ *missingqs = ulis[6]; /* number of missing quartets */ PP_quartrecved += *numofq; PP_quartrecvedn++; truenum = (uli)((*numofq+1)/2); trueaddr = (unsigned char *)(quartetinfo + (uli)(*startq/2)); # ifdef PVERBOSE3 fprintf(STDOUT, "(%2d) ... Recv QuartBlockSpecs (%ld, %ld, %ld, %d)\n", PP_Myid, ulis[0], ulis[1], ulis[2], ints[0]); # endif /* PVERBOSE3 */ DtypelensRes[0] = truenum; MPI_Address(trueaddr, DtypeaddrRes); bq = calloc((size_t) *numofbq, sizeof(uli)); DtypelensRes[1] = *numofbq; MPI_Address(bq, (DtypeaddrRes+1)); MPI_Type_struct(2, DtypelensRes, DtypeaddrRes, DtypesRes, &PP_QBlockRes); MPI_Type_commit(&PP_QBlockRes); error = MPI_Recv(MPI_BOTTOM, 1, PP_QBlockRes, dest, PP_QUARTBLOCK, PP_Comm, &stat); if (error != MPI_SUCCESS) PP_Printerror(STDOUT, PP_Myid, error); # ifdef PVERBOSE3 fprintf(STDOUT, "(%2d) ... Recv QuartBlock \n", PP_Myid); # endif /* PVERBOSE3 */ /* MPI package check */ qstart = *startq; qend = qstart + *numofq - 1; for (i = 3; i < Maxspc; i++) for (c = 2; c < i; c++) for (b = 1; b < c; b++) for (a = 0; a < b; a++) { /* use a better way, not computing this every time */ idx = (uli) a + (uli) b*(b-1)/2 + (uli) c*(c-1)*(c-2)/6 + (uli) i*(i-1)*(i-2)*(i-3)/24; if ((idx >= qstart) && (idx <= qend)) { quartettype = readquartet(a,b,c,i); switch(quartettype) { case 1: /* 001 */ case 2: /* 010 */ case 4: /* 100 */ { tmpfullresqs++; /* number of fully resolved quartets */ break; } case 3: /* 011 */ case 5: /* 101 */ case 6: /* 110 */ { tmppartresqs++; /* number of partly resolved quartets */ break; } case 7: /* 111 */ { tmpunresqs++; /* number of unresolved quartets */ #if 0 /* to make the part below obsolete */ badqs++; badtaxon[a]++; badtaxon[b]++; badtaxon[c]++; badtaxon[d]++; if (show_optn) { fputid10(unresfp, a); fprintf(unresfp, " "); fputid10(unresfp, b); fprintf(unresfp, " "); fputid10(unresfp, c); fprintf(unresfp, " "); fputid(unresfp, d); fprintf(unresfp, "\n"); } #endif break; } case 0: /* 000 */ default: { tmpmissingqs++; /* number of missing quartets */ break; } } /* end switch quartettype */ } /* if idx */ } /* for for for for */ /* end MPI package check */ if((tmpfullresqs != *fullresqs) || (tmppartresqs != *partresqs) || (tmpunresqs != *unresqs) || (tmpmissingqs != *missingqs)) { fprintf(stderr, "ERROR: Quartets differ between send and receive!!! (received/sent)\n"); fprintf(stderr, "fully (%lu/%lu), partly(%lu/%lu), unresolved(%lu/%lu), missing(%lu/%lu)\n", tmpfullresqs, *fullresqs, tmppartresqs, *partresqs, tmpunresqs, *unresqs, tmpmissingqs, *missingqs); } PP_putslave(dest); for(count = 0; count < *numofbq; count++){ int a, b, c, d; num2quart(bq[count], &a, &b, &c, &d); # ifdef PVERBOSE2 fprintf(STDOUT, "(%2d) %ld. bad quarted (%d, %d, %d, %d) = %ld\n", PP_Myid, count, a, b, c, d, bq[count]); # endif /* PVERBOSE2 */ badqs++; badtaxon[a]++; badtaxon[b]++; badtaxon[c]++; badtaxon[d]++; if (show_optn) { fputid10(unresfp, a); fprintf(unresfp, " "); fputid10(unresfp, b); fprintf(unresfp, " "); fputid10(unresfp, c); fprintf(unresfp, " "); fputid(unresfp, d); fprintf(unresfp, "\n"); } } free(bq); MPI_Type_free(&PP_QBlockSpecs); MPI_Type_free(&PP_QBlockRes); # ifdef PVERBOSE2 fprintf(STDOUT, "(%2d) <- (%2d) ... Recv xxPP_QuartBlock(0,%lu)=%d,%d\n", PP_Myid, dest, truenum-1, trueaddr[0], trueaddr[truenum-1]); # endif /* PVERBOSE2 */ # undef NUMULI # undef NUMINT } /* PP_RecvQuartBlock */ /********************************************************************* * send/receive array with all quartets (M->S) * *********************************************************************/ void PP_SendAllQuarts(unsigned long Numquartets, unsigned char *quartetinfo) { MPI_Datatype Dtypes[1] = {MPI_UNSIGNED_CHAR}; int Dtypelens[1]; MPI_Aint Dtypeaddr[1]; MPI_Datatype PP_AllQuarts; int dest; int error; # ifdef PVERBOSE2 fprintf(STDOUT, "(%2d) Sending: PP_AllQuart(0)=%d\n", PP_Myid, quartetinfo[0]); # endif /* PVERBOSE2 */ /* compute number of quartets */ if (Numquartets % 2 == 0) { /* even number */ Dtypelens[0] = (Numquartets)/2; } else { /* odd number */ Dtypelens[0] = (Numquartets + 1)/2; } MPI_Address(&(quartetinfo[0]), Dtypeaddr); MPI_Type_struct(1, Dtypelens, Dtypeaddr, Dtypes, &PP_AllQuarts); MPI_Type_commit(&PP_AllQuarts); for (dest=1; dest (%2d) ... Sent xxAllQuart(0,%d)=%d,%d (%luq -> %db)\n", PP_Myid, dest, Dtypelens[0]-1, quartetinfo[0], quartetinfo[Dtypelens[0]-1], Numquartets, Dtypelens[0]-1); # endif /* PVERBOSE3 */ } /* for each slave */ MPI_Type_free(&PP_AllQuarts); } /* PP_SendAllQuarts */ /******************/ void PP_RecvAllQuarts(int taxa, unsigned long *Numquartets, unsigned char *quartetinfo) { MPI_Datatype Dtypes[1] = {MPI_UNSIGNED_CHAR}; int Dtypelens[1]; MPI_Aint Dtypeaddr[1]; MPI_Datatype PP_AllQuarts; MPI_Status stat; int error; # ifdef PVERBOSE3 fprintf(STDOUT, "(%2d) Receiving AllQuarts ...\n", PP_Myid); # endif /* PVERBOSE3 */ /* compute number of quartets */ *Numquartets = (uli) taxa*(taxa-1)*(taxa-2)*(taxa-3)/24; if (*Numquartets % 2 == 0) { /* even number */ Dtypelens[0] = (*Numquartets)/2; } else { /* odd number */ Dtypelens[0] = (*Numquartets + 1)/2; } MPI_Address(&(quartetinfo[0]), Dtypeaddr); MPI_Type_struct(1, Dtypelens, Dtypeaddr, Dtypes, &PP_AllQuarts); MPI_Type_commit(&PP_AllQuarts); error = MPI_Recv(MPI_BOTTOM, 1, PP_AllQuarts, PP_MyMaster, PP_ALLQUARTS, PP_Comm, &stat); if (error != MPI_SUCCESS) PP_Printerror(STDOUT, 1300+PP_Myid, error); MPI_Type_free(&PP_AllQuarts); # ifdef PVERBOSE2 fprintf(STDOUT, "(%2d) <- (%2d) ... Recv xxAllQuart(0,%d)=%d,%d (%luq -> %db)\n", PP_Myid, PP_MyMaster, Dtypelens[0]-1, quartetinfo[0], quartetinfo[Dtypelens[0]-1], *Numquartets, Dtypelens[0]-1); # endif /* PVERBOSE2 */ } /* PP_RecvAllQuarts */ /********************************************************************* * procedures to send the splits of a puzzle tree to the master * *********************************************************************/ void PP_SendSplitsBlock(int taxa, uli blocksize, cmatrix *biparts, int pstnum, treelistitemtype *pstlist) { MPI_Datatype *Dtypes; int *Dtypelens; MPI_Aint *Dtypeaddr; MPI_Datatype PP_Biparts; int error; int n; int ints[3]; int *pstnumarr; treelistitemtype *pstptr; PP_splitsent+=blocksize; PP_splitsentn++; ints[0] = taxa; ints[1] = (int) blocksize; ints[2] = pstnum; error = MPI_Ssend(ints, 3, MPI_INT, PP_MyMaster, PP_PUZZLEBLOCKSPECS, PP_Comm); if (error != MPI_SUCCESS) PP_Printerror(STDOUT, 1800+PP_Myid, error); Dtypes = calloc((size_t) (blocksize + pstnum + 1), sizeof(MPI_Datatype)); Dtypelens = calloc((size_t) (blocksize + pstnum + 1), sizeof(int)); Dtypeaddr = calloc((size_t) (blocksize + pstnum + 1), sizeof(MPI_Aint)); pstnumarr = calloc((size_t) pstnum, sizeof(int)); # ifdef PVERBOSE2 fprintf(STDOUT, "(%2d) Sending: PP_bipartsblock(0..%lu,0,0)8=\"%c\"\n", PP_Myid, blocksize, biparts[0][0][0]); # endif /* PVERBOSE2 */ for (n=0; n<(int)blocksize; n++) { Dtypes[n] = MPI_CHAR; Dtypelens[n] = (taxa - 3) * taxa; MPI_Address(&(biparts[n][0][0]), &(Dtypeaddr[n])); } pstptr = pstlist; for (n=0; n%d: [%d/%d] #=%d \"%s\"\n", PP_Myid, PP_MyMaster, n, pstnum, pstnumarr[n], (*pstptr).tree); # endif /* PVERBOSE3 */ pstptr = (*pstptr).succ; } Dtypes[((int)blocksize + pstnum)] = MPI_INT; Dtypelens[((int)blocksize + pstnum)] = pstnum; MPI_Address(&(pstnumarr[0]), &(Dtypeaddr[((int)blocksize + pstnum)])); MPI_Type_struct(((int)blocksize + pstnum + 1), Dtypelens, Dtypeaddr, Dtypes, &PP_Biparts); MPI_Type_commit(&PP_Biparts); error = MPI_Ssend(MPI_BOTTOM, 1, PP_Biparts, PP_MyMaster, PP_PUZZLEBLOCK, PP_Comm); if (error != MPI_SUCCESS) PP_Printerror(STDOUT, 1800+PP_Myid, error); MPI_Type_free(&PP_Biparts); free(Dtypes); free(Dtypelens); free(Dtypeaddr); free(pstnumarr); # ifdef PVERBOSE3 fprintf(STDOUT, "(%2d) ... Sent PP_bipartsblock\n", PP_Myid); # endif /* PVERBOSE3 */ } /* PP_SendSplitsBlock */ /******************/ void PP_RecvSplitsBlock(int *taxa, uli *blocksize, cmatrix **bip, treelistitemtype **pstlist, int *pstnum, int *pstsum) /* bp -> (*bip) */ { MPI_Datatype *Dtypes; int *Dtypelens; MPI_Aint *Dtypeaddr; MPI_Datatype PP_Biparts; MPI_Status stat; int error; int n; int dest; int ints[3]; int pstlistnum; int tmpnum; int tmpsum; int *pstnumarr; char **pstarr; treelistitemtype *treeitem; error = MPI_Recv(ints, 3, MPI_INT, MPI_ANY_SOURCE, PP_PUZZLEBLOCKSPECS, PP_Comm, &stat); if (error != MPI_SUCCESS) PP_Printerror(STDOUT, 1900+PP_Myid, error); dest = stat.MPI_SOURCE; *taxa = ints[0]; *blocksize = (uli) ints[1]; pstlistnum = ints[2]; # ifdef PVERBOSE2 fprintf(STDOUT, "(%2d) Received<-%d: PP_bipartsblockspec(t=%d,b=%ld,p=%d)\n", PP_Myid, dest, *taxa, *blocksize, pstlistnum); # endif /* PVERBOSE2 */ PP_splitrecved += *blocksize; PP_splitrecvedn++; Dtypes = calloc((size_t) (*blocksize + pstlistnum + 1), sizeof(MPI_Datatype)); Dtypelens = calloc((size_t) (*blocksize + pstlistnum + 1), sizeof(int)); Dtypeaddr = calloc((size_t) (*blocksize + pstlistnum + 1), sizeof(MPI_Aint)); (*bip) = (cmatrix *) calloc((size_t) *blocksize, sizeof(void *)); pstnumarr = (int *) calloc((size_t) pstlistnum, sizeof(int)); pstarr = (char **) calloc((size_t) pstlistnum, sizeof(char *)); /* pstarr[0] = (char *) calloc((size_t) (psteptreestrlen * pstlistnum), sizeof(char)); for(n=1; n requests and receive results */ void PP_SendDoPermutBlock(uli puzzlings) { int dest; /* destination process */ int error; /* MPI error code */ uli numpuzzlings; /* puzzlings scheduled for 1 chunk */ uli puzzlingssent = 0; /* puzzlings we are waiting for */ schedtype sched; /* scheduler data */ uli bipnum; /* bipartition counter */ int tx; /* number of received trees */ uli bs; /* number of received split sets */ cmatrix *bp; /* split sets */ initsched(&sched, puzzlings, PP_NumProcs-1, 4); /* numpuzzlings = sc(&sched); */ numpuzzlings = SCHEDALG_PUZZLING(&sched); # ifdef SCHED_DEBUG if ((numpuzzlings < 4) && (numpuzzlings != 0)) fprintf(stderr, "SCHED-ERROR: %d < 4 (puzzling) !!!", numpuzzlings); # endif /* SCHED_DEBUG */ while (numpuzzlings > 0) { if (PP_emptyslave()) { PP_RecvSplitsBlock(&tx, &bs, &bp, &psteptreelist, &psteptreenum, &psteptreesum); for (bipnum=0; bipnum 0) { /* receive next result */ PP_RecvSplitsBlock(&tx, &bs, &bp, &psteptreelist, &psteptreenum, &psteptreesum); /* file splits */ for (bipnum=0; bipnum%4ld (%dx%ld)\n", PP_Myid, qstart, qend, PP_NumProcs-1, qtodo); # endif addtimes(GENERAL, &tarr); for (i = 3; i < Maxspc; i++) for (c = 2; c < i; c++) for (b = 1; b < c; b++) for (a = 0; a < b; a++) { /* use a better way, not computing this every time */ idx = (uli) a + (uli) b*(b-1)/2 + (uli) c*(c-1)*(c-2)/6 + (uli) i*(i-1)*(i-2)*(i-3)/24; if ((idx >= qstart) && (idx <= qend)) { # ifdef PVERBOSE4 fprintf(STDOUT, "(%2d) %4ld <---> (%d,%d,%d,%d)\n",PP_Myid, idx, a,b,c,i); # endif compute_quartlklhds(a,b,c,i,&d1,&d2,&d3,approx); quartettype = PP_do_write_quart(a,b,c,i,d1,d2,d3,&nofbq,bqarr,usebestq); switch(quartettype) { case 1: /* 001 */ case 2: /* 010 */ case 4: /* 100 */ { fullresqs++; /* number of fully resolved quartets */ break; } case 3: /* 011 */ case 5: /* 101 */ case 6: /* 110 */ { partresqs++; /* number of partly resolved quartets */ break; } case 7: /* 111 */ { unresqs++; /* number of unresolved quartets */ break; } case 0: /* 000 */ default: { missingqs++; /* number of missing quartets */ break; } } /* end switch quartettype */ addtimes(QUARTETS, &tarr); } /* if idx */ } /* for for for for */ PP_SendQuartBlock(qstart, qtodo, quartetinfo, fullresqs, partresqs, unresqs, missingqs, nofbq, bqarr, usebestq, approx); free(bqarr); bqarr=NULL; break; } case PP_DOPUZZLEBLOCK: { if (PP_AllQuartsReceived){ uli numtrial; /* receive number of steps to perform */ PP_RecvDoPermutBlock(&numtrial); allpstep(numtrial, quartetinfo, Maxspc, fixedorder_optn); } else { fprintf(STDOUT, "ERROR: Requested Puzzle Tree without receiving Quartets!!!\n"); notdone = 0; } break; } case PP_DOQUART: { PP_RecvDoQuart(&a,&b,&c,&d, &usebestq, &approx); addtimes(GENERAL, &tarr); compute_quartlklhds(a,b,c,d,&d1,&d2,&d3,approx); addtimes(QUARTETS, &tarr); PP_SendQuart(a,b,c,d,d1,d2,d3, usebestq, approx); break; } default: { fprintf(STDOUT, "ERROR: Unknown Message Tag received\n"); MPI_Abort(PP_Comm, 1); } } /* switch stat.MPI_TAG */ MPI_Probe(PP_MyMaster, MPI_ANY_TAG, PP_Comm, &stat); notdone = (stat.MPI_TAG != PP_DONE); if (!notdone) PP_RecvDone(); } /* while notdone */ return (0); } /* slave_main */ tree-puzzle-5.2/src/ppuzzle.h0000644000076400001440000002577410073365416012024 /* * ppuzzle.h * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifndef _PPUZZLE_ #define _PPUZZLE_ /* #include "treesort.h" */ #include "puzzle.h" #include "util.h" #include "ml.h" #include "sched.h" extern int PP_IamSlave; extern int PP_IamMaster; #ifdef PARALLEL # ifdef SEQUENTIAL # undef SEQUENTIAL # endif # define SEQUENTIAL 0 # undef PARALLEL # define PARALLEL 1 # include "mpi.h" #else # ifdef SEQUENTIAL # undef SEQUENTIAL # endif # define SEQUENTIAL 1 # define PARALLEL 0 # undef PVERBOSE # undef PVERBOSE1 # undef PVERBOSE2 # undef PVERBOSE3 #endif /* PVERBOSE3 includes PVERBOSE2 includes PVERBOSE1 */ /* PVERBOSE1 is default (PVERBOSE) */ #ifdef PVERBOSE # undef PVERBOSE1 # define PVERBOSE1 #endif #ifdef PVERBOSE3 # undef PVERBOSE2 # define PVERBOSE2 #endif #ifdef PVERBOSE2 # undef PVERBOSE1 # define PVERBOSE1 #endif #if PARALLEL /* Scheduling algorithms for: */ # define SCHEDALG_PARAM_EST sgss /* Parameter estimation */ # define SCHEDALG_ML_STEP sgss /* ML step */ # define SCHEDALG_PUZZLING sgss /* puzzling step */ # define PP_DONE 0 /* Finished M->S */ # define PP_SIZES 1 /* Array sizes needed M->S */ # define PP_DATA 2 /* Data Arrays M->S */ # define PP_ALLQUARTS 3 /* All Quartets M->S */ # define PP_DOQUART 4 /* do 4Specs M->S */ # define PP_DOQUARTX2 5 /* do 4Specs + X^2 M->S */ # define PP_QUART 6 /* quartet back S->M */ # define PP_QUARTX2 7 /* quartet + X^2 back S->M */ # define PP_DOQUARTBLOCKSPECS 8 /* do block Specs M->S */ # define PP_DOQUARTBLOCK 9 /* do block of Quarts M->S */ # define PP_QUARTBLOCKSPECS 10 /* block Specs S->M */ # define PP_QUARTBLOCK 11 /* block of Quarts S->M */ # define PP_DOPUZZLE 12 /* do Puzzling step M->S, obsolete (HAS)*/ # define PP_PUZZLE 13 /* Puzzling tree back S->M, obsolete (HAS)*/ # define PP_DOPUZZLEBLOCK 14 /* do Puzzling block M->S */ # define PP_DOPUZZLEBLOCKSPECS 15 /* do Puzzling block M->S */ # define PP_PUZZLEBLOCK 16 /* Puzzling block S->M */ # define PP_PUZZLEBLOCKSPECS 17 /* Puzzling block S->M */ # define PP_STATS 18 /* Slave Statistics S->M */ # define PP_WAIT 19 /* waiting for work S->M */ # define PP_MLDISTANCE 20 /* start mldistance M->S */ /*epe*/ # define PP_UPDATERATES 21 /* update Rates M->S */ /*epe*/ # define PP_UPDATEFRACINV 22 /* update fracinv M->S */ /*epe*/ # define PP_UPDATEEEI 23 /* update Eval,Evec, Ievc M->S */ /*epe*/ # define PP_NOUPDATE 24 /* update nothing and start with scatter operation M->S */ /*epe*/ # define PP_FINALUPDATE 25 /* updates Rates, fracinv, EEI, Distanmat M->S */ /*epe*/ # define PP_LSLENGTH 26 /* parallelization of lslength() M->S */ /*epe*/ # define PP_TEST 100 /* testing */ # define PERMUTQUEUESIZE 100 # define QUARTQUEUESIZE 100 extern int PP_IamMaster; extern int PP_IamSlave; extern int PP_Myid; extern int PP_MyMaster; extern int PP_NumProcs; extern MPI_Comm PP_Comm; #endif /* PARALLEL */ extern int *permutsent, *permutrecved, *quartsent, *quartrecved, *doquartsent, *doquartrecved, *splitsent, *splitrecved, *permutsentn, *permutrecvedn, *quartsentn, *quartrecvedn, *doquartsentn, *doquartrecvedn, *splitsentn, *splitrecvedn; extern double *walltimes, *cputimes; extern double *fullwalltimes, *fullcputimes; extern double *altwalltimes, *altcputimes; extern int PP_permutsent, PP_permutrecved, PP_quartsent, PP_quartrecved, PP_doquartsent, PP_doquartrecved, PP_splitsent, PP_splitrecved, PP_permutsentn, PP_permutrecvedn, PP_quartsentn, PP_quartrecvedn, PP_doquartsentn, PP_doquartrecvedn, PP_splitsentn, PP_splitrecvedn; extern double PP_starttime, PP_stoptime, PP_inittime, PP_paramcomptime, PP_paramsendtime, PP_quartcomptime, PP_quartsendtime, PP_puzzletime, PP_treetime; void num2quart(uli qnum, int *a, int *b, int *c, int *d); uli numquarts(int maxspc); uli quart2num (int a, int b, int c, int d); int slave_main(int argc, char *argv[]); void PP_Init(int *argc, char **argv[]); void PP_Finalize(); void PP_Printerror(FILE *of, int id, int err); void PP_RecvDoQuart(int *a, int *b, int *c, int *d, int *usebestq, int *approx); void PP_SendDoQuart(int dest, int a, int b, int c, int d, int usebestq, int approx); void PP_RecvQuart(int *a, int *b, int *c, int *d, double *d1, double *d2, double *d3, int *usebestq, int *approx); void PP_SendQuart(int a, int b, int c, int d, double d1, double d2, double d3, int usebestq, int approx); void PP_SendSizes(int mspc, /* Maxspc */ int msite, /* Maxsite */ int ncats, /* numcats */ int nptrn, /* Numptrn */ int rad, /* tpmradix */ int outgr, /* outgroup */ double frconst, /* fracconst */ int rseed, /* randseed */ int fixedorder, /* fixedorder_optn */ int consensus); /* consensus_optn */ void PP_RecvSizes(int *mspc, /* Maxspc */ int *msite, /* Maxsite */ int *ncats, /* numcats */ int *nptrn, /* Numptrn */ int *rad, /* tpmradix */ int *outgr, /* outgroup */ double *frconst, /* fracconst */ int *rseed, /* randseed */ int *fixedorder, /* fixedorder_optn */ int *consensus); /* consensus_optn */ void PP_RecvData( cmatrix Seqpat, /* cmatrix (Maxspc x Numptrn) */ ivector Alias, /* ivector (Maxsite) */ ivector Weight, /* ivector (Numptrn) */ ivector constpat, dvector Rates, /* dvector (numcats) */ dvector Eval, /* dvector (tpmradix) */ dvector Freqtpm, dmatrix Evec, /* dmatrix (tpmradix x tpmradix) */ dmatrix Ievc, dmatrix iexp, /* dmatrix Distanmat,*/ /*epe*/ /* dmatrix (Maxspc x Maxspc) */ dcube ltprobr); /* dcube (numcats x tpmradix x tpmradix) */ void PP_SendData( cmatrix Seqpat, /* cmatrix (Maxspc x Numptrn) */ ivector Alias, /* ivector (Maxsite) */ ivector Weight, /* ivector (Numptrn) */ ivector constpat, dvector Rates, /* dvector (numcats) */ dvector Eval, /* dvector (tpmradix) */ dvector Freqtpm, dmatrix Evec, /* dmatrix (tpmradix x tpmradix) */ dmatrix Ievc, dmatrix iexp, /* dmatrix Distanmat,*/ /*epe*/ /* dmatrix (Maxspc x Maxspc) */ dcube ltprobr); /* dcube (numcats x tpmradix x tpmradix) */ void PP_SendAllQuarts(unsigned long Numquartets, unsigned char *quartetinfo); void PP_RecvAllQuarts(int taxa, unsigned long *Numquartets, unsigned char *quartetinfo); void PP_SendDoQuartBlock(int dest, uli firstq, uli amount, int usebestq, int approx); void PP_RecvDoQuartBlock(uli *firstq, uli *amount, uli **bq, int *usebestq, int *approx); void PP_SendQuartBlock(uli startq, uli numofq, unsigned char *quartetinfo, uli fullresqs, /* number of fully resolved quartets */ uli partresqs, /* number of partly resolved quartets */ uli unresqs, /* number of unresolved quartets */ uli missingqs, /* number of missing quartets */ uli numofbq, uli *bq, int usebestq, int approx); void PP_RecvQuartBlock(int slave, uli *startq, uli *numofq, unsigned char *quartetinfo, uli *fullresqs, /* number of fully resolved quartets */ uli *partresqs, /* number of partly resolved quartets */ uli *unresqs, /* number of unresolved quartets */ uli *missingqs, /* number of missing quartets */ int *usebestq, int *approx); void PP_SendDoPermutBlock(uli puzzlings); void PP_RecvDoPermutBlock(uli *taxa); void PP_SendSplitsBlock(int taxa, uli blocksize, cmatrix *biparts, int pstnum, treelistitemtype *pstlist); void PP_SendDone(); void PP_RecvDone(); int PP_emptyslave(); void PP_putslave(int sl); int PP_getslave(); void PP_cmpd(int rank, double a, double b); void PP_cmpi(int rank, int a, int b); /*epe*/ void PP_NextCoord(int* x, int* y, int chunk); void PP_NextCoord_atamt(int* x, int* y, int chunk, int dimen); void PP_VectorToDM(int x, int y, int chunk, double* result); void PP_DMToVector(int x, int y, int chunk, double* result); void PP_Update_Rates(); void PP_Update_fracinv(); void PP_Update_EEI(); void PP_NoUpdate(); void PP_Final_Update(void); #endif /* _PPUZZLE_ */ tree-puzzle-5.2/src/subsetmatr.c0000644000076400001440000001463610073365422012467 /* * subsetmatr.c * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #include "subsetmatr.h" /**********************/ void chooserfromsubsets(cmatrix ssmatr, imatrix sssets, ivector sssizes, int numsets, int numspecs, ivector permutation) { int i; int currset, currspec; int currid; int first; int setsize, setfreesize, setcount, speccount; ivector isfreespec, isfreeset, freeinsubset, subsetoverlap; isfreespec = new_ivector(numspecs); for (i = 0; i < numspecs; i++) isfreespec[i] = TRUE; isfreeset = new_ivector(numsets); for (i = 0; i < numsets; i++) isfreeset[i] = TRUE; freeinsubset = new_ivector(numspecs); subsetoverlap = new_ivector(numsets); for (i = 0; i < numsets; i++) subsetoverlap[i] = 0; for (i = 0; i < numsets; i++) isfreeset[i] = TRUE; currid = 0; first = TRUE; for (setcount=0; setcount= 3) || first))); fprintf(stderr, " %3d. %3d (OVL:%d)\n", setcount, currset, subsetoverlap[currset]); first = FALSE; isfreeset[currset] = FALSE; setsize = sssizes[currset]; setfreesize = 0; for (speccount=0; speccount= 100) { fprintf(stdout, " | "); for (n1 = 0; n1 < subsets; n1++) { x = (n1-(n1%100))/100; if (x != 0) fprintf(stdout, "%2d", x); else fprintf(stdout, "%2c", ' '); } fprintf(stdout, "\n"); } if (subsets >= 10) { fprintf(stdout, " | "); for (n1 = 0; n1 < subsets; n1++) { x = (n1-(n1%10))/10; if (x != 0) fprintf(stdout, "%2d", x); else fprintf(stdout, "%2c", ' '); } fprintf(stdout, "\n"); } fprintf(stdout, "seq | "); for (n1 = 0; n1 < subsets; n1++) fprintf(stdout, "%2d", n1%10); fprintf(stdout, "\n"); fprintf(stdout, "----+-"); for (n1 = 0; n1 < subsets; n1++) fprintf(stdout, "--"); fprintf(stdout, "\n"); for (n2 = 0; n2 < seqs; n2++) { fprintf(stdout, "s%3d| ", n2); for (n1 = 0; n1 < subsets; n1++) { fprintf(stdout, "%2c", ((1 == subsetmatr[n1][n2]) ? 'X' : '.')); } fprintf(stdout, "\n"); } } /* printssmatr */ /**********************/ void readssmatr(FILE *fp, cmatrix *ssmatr, imatrix *sslists, ivector *sssizes, int *subsets, int *seqs) { int setcount, speccount; *subsets = 0; *seqs = 0; /* read matrix coordinate sizes from file */ fscanf(fp, "%d", subsets); fscanf(fp, "%d", seqs); printf("subsets: %d - seqs: %d\n\n", *subsets, *seqs); /* read to begin of the binary format matrix */ while ('\n' != getc(fp)); /* allocate memory */ *ssmatr = new_cmatrix(*subsets, *seqs); *sslists = new_imatrix(*subsets, *seqs); *sssizes = new_ivector(*subsets); /* initialze values */ for (setcount = 0; setcount < *subsets; setcount++){ (*sssizes)[setcount] = 0; for (speccount = 0; speccount < *seqs; speccount++){ (*sslists)[setcount][speccount] = *seqs; } /* for speccount */ } /* for setcount */ /* read matrix from file */ if((*subsets) * (*seqs) != fread(&((*ssmatr)[0][0]), sizeof(char), (*subsets) * (*seqs), fp)) { fprintf(stderr, "ERROR reading subset matrix from file!!!\n"); exit(1); } /* create subset lists/sizes */ for (setcount = 0; setcount < *subsets; setcount++){ for (speccount = 0; speccount < *seqs; speccount++){ if ((*ssmatr)[setcount][speccount] == 1) { (*sslists)[setcount][((*sssizes)[setcount])] = speccount; ((*sssizes)[setcount])++; } /* ssmatr == 1 */ } /* for speccount */ } /* for setcount */ } /* readssmatr */ /**********************/ void writessmatr(FILE *fp, cmatrix subsetmatr, int subsets, int seqs) { fprintf(fp, " %d %d \n", subsets, seqs); if(subsets*seqs != fwrite(&(subsetmatr[0][0]), sizeof(char), subsets*seqs, fp)) { fprintf(stderr, "ERROR writing subset matrix to file!!!\n"); exit(1); } } /* writessmatr */ tree-puzzle-5.2/src/subsetmatr.h0000644000076400001440000000202710073365425012466 /* * subsetmatr.h * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifndef SUBSETMATR_H #define SUBSETMATR_H #include #include #include "util.h" void printssmatr(cmatrix subsetmatr, int subsets, int seqs); void printsubsets(imatrix sssets, ivector sssizes, int subsets, int seqs); void readssmatr(FILE *fp, cmatrix *ssmatr, imatrix *sslists, ivector *sssizes, int *subsets, int *seqs); void writessmatr(FILE *fp, cmatrix subsetmatr, int subsets, int seqs); void chooserfromsubsets(cmatrix ssmatr, imatrix sssets, ivector sssizes, int numsets, int numspecs, ivector trueid); #endif /* SUBSETMATR_H */ tree-puzzle-5.2/src/pstep-mrca.c0000644000076400001440000005270110073365430012343 /* * pstep-mrca.c * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifdef HAVE_CONFIG_H # include #endif #define EXTERN extern #include #include #include"puzzle.h" /* #include"util.h" */ /* #include"pstep.h" */ /******************************************************************************/ /* functions for representing and building puzzling step trees */ /******************************************************************************/ /* initialize tree with the following starting configuration * A(=0) * [up =NULL] * [downleft =1] * [downright=2] * * o * | * | * +-------------+--------------+ * | | * | | * o o * * C(=1) B(=2) * [up =0] [up =0] * [downleft =NULL] [downleft =NULL] * [downright=NULL] [downright=NULL] * * nextedge = 3 * nextleaf = 3 * and set according edge maps * */ void inittree_orig(ONEEDGE_ORIG **edge, /* out: new array of edges */ int **edgeofleaf,/* out: array of external edge ptrs */ int Maxspc, /* in: Number of species (n) */ int Maxbrnch, /* in: Number of branches (2n-3) */ int *nextedge, /* out: next free edge index (=3) */ int *nextleaf) /* out: next free leaf index (=3) */ { int i; ONEEDGE_ORIG *tmpedge; int *tmpedgeofleaf; /* allocate the memory for the whole tree */ /* allocate memory for vector with all the edges of the tree */ tmpedge = (ONEEDGE_ORIG *) calloc((size_t) Maxbrnch, sizeof(ONEEDGE_ORIG) ); if (tmpedge == NULL) maerror("edge in inittree"); *edge = tmpedge; /* allocate memory for vetmpctor with edge numbers of leaves */ tmpedgeofleaf = (int *) calloc((size_t) Maxspc, sizeof(int) ); if (tmpedgeofleaf == NULL) maerror("edgeofleaf in inittree"); *edgeofleaf = tmpedgeofleaf; /* allocate memory for all the edges the edge map */ for (i = 0; i < Maxbrnch; i++) { (tmpedge)[i].edgemap = (int *) calloc((size_t) Maxbrnch, sizeof(int) ); if (tmpedge[i].edgemap == NULL) maerror("edgemap in inittree"); } /* number all edges */ for (i = 0; i < Maxbrnch; i++) tmpedge[i].numedge = i; /* initialize tree */ *nextedge = 3; *nextleaf = 3; /* edge maps */ (tmpedge[0].edgemap)[0] = 0; /* you are on the right edge */ (tmpedge[0].edgemap)[1] = 4; /* go down left for leaf 1 */ (tmpedge[0].edgemap)[2] = 5; /* go down right for leaf 2 */ (tmpedge[1].edgemap)[0] = 1; /* go up for leaf 0 */ (tmpedge[1].edgemap)[1] = 0; /* you are on the right edge */ (tmpedge[1].edgemap)[2] = 3; /* go up/down right for leaf 2 */ (tmpedge[2].edgemap)[0] = 1; /* go up for leaf 0 */ (tmpedge[2].edgemap)[1] = 2; /* go up/down left for leaf 1 */ (tmpedge[2].edgemap)[2] = 0; /* you are on the right edge */ /* interconnection */ tmpedge[0].up = NULL; tmpedge[0].downleft = &tmpedge[1]; tmpedge[0].downright = &tmpedge[2]; tmpedge[1].up = &tmpedge[0]; tmpedge[1].downleft = NULL; tmpedge[1].downright = NULL; tmpedge[2].up = &tmpedge[0]; tmpedge[2].downleft = NULL; tmpedge[2].downright = NULL; /* edges of leaves */ tmpedgeofleaf[0] = 0; tmpedgeofleaf[1] = 1; tmpedgeofleaf[2] = 2; } /* inittree */ /******************/ /* add next leaf on the specified edge */ void addnextleaf_orig(int dockedge, /* insert here */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc, /* No. of species */ int Maxbrnch, /* No. of branches */ int *in_nextedge, /* next free edge idx */ int *in_nextleaf) /* next free leaf idx */ { int i; int nextedge; int nextleaf; nextedge=*in_nextedge; nextleaf=*in_nextleaf; if (dockedge >= nextedge) { /* Trying to add leaf nextleaf to nonexisting edge dockedge */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR F TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } if (nextleaf >= Maxspc) { /* Trying to add leaf nextleaf to a tree with Maxspc leaves */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR G TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } /* necessary change in edgeofleaf if dockedge == edgeofleaf[0] */ if (edgeofleaf[0] == dockedge) edgeofleaf[0] = nextedge; /* adding nextedge to the tree */ edge[nextedge].up = edge[dockedge].up; edge[nextedge].downleft = &edge[dockedge]; edge[nextedge].downright = &edge[nextedge+1]; edge[dockedge].up = &edge[nextedge]; if (edge[nextedge].up != NULL) { if ( ((edge[nextedge].up)->downleft) == &edge[dockedge] ) (edge[nextedge].up)->downleft = &edge[nextedge]; else (edge[nextedge].up)->downright = &edge[nextedge]; } /* adding nextedge + 1 to the tree */ edge[nextedge+1].up = &edge[nextedge]; edge[nextedge+1].downleft = NULL; edge[nextedge+1].downright = NULL; edgeofleaf[nextleaf] = nextedge+1; /* the two new edges get info about the old edges */ /* nextedge */ for (i = 0; i < nextedge; i++) { switch ( (edge[dockedge].edgemap)[i] ) { /* down right changes to down left */ case 5: (edge[nextedge].edgemap)[i] = 4; break; /* null changes to down left */ case 0: (edge[nextedge].edgemap)[i] = 4; break; default:(edge[nextedge].edgemap)[i] = (edge[dockedge].edgemap)[i]; break; } } /* nextedge + 1 */ for (i = 0; i < nextedge; i++) { switch ( (edge[dockedge].edgemap)[i] ) { /* up/down left changes to up */ case 2: (edge[nextedge+1].edgemap)[i] = 1; break; /* up/down right changes to up */ case 3: (edge[nextedge+1].edgemap)[i] = 1; break; /* down left changes to up/down left */ case 4: (edge[nextedge+1].edgemap)[i] = 2; break; /* down right changes to up/down left */ case 5: (edge[nextedge+1].edgemap)[i] = 2; break; /* null changes to up/down left */ case 0: (edge[nextedge+1].edgemap)[i] = 2; break; /* up stays up */ default:(edge[nextedge+1].edgemap)[i] = (edge[dockedge].edgemap)[i]; break; } } /* dockedge */ for (i = 0; i < nextedge; i++) { switch ( (edge[dockedge].edgemap)[i] ) { /* up/down right changes to up */ case 3: (edge[dockedge].edgemap)[i] = 1; break; /* up/down left changes to up */ case 2: (edge[dockedge].edgemap)[i] = 1; break; default: break; } } /* all edgemaps are updated for the two new edges */ /* nextedge */ (edge[nextedge].edgemap)[nextedge] = 0; (edge[nextedge].edgemap)[nextedge+1] = 5; /* down right */ /* nextedge + 1 */ (edge[nextedge+1].edgemap)[nextedge] = 1; /* up */ (edge[nextedge+1].edgemap)[nextedge+1] = 0; /* all other edges */ for (i = 0; i < nextedge; i++) { (edge[i].edgemap)[nextedge] = (edge[i].edgemap)[dockedge]; (edge[i].edgemap)[nextedge+1] = (edge[i].edgemap)[dockedge]; } /* an extra for dockedge */ (edge[dockedge].edgemap)[nextedge] = 1; /* up */ (edge[dockedge].edgemap)[nextedge+1] = 3; /* up/down right */ nextleaf++; nextedge = nextedge + 2; *in_nextedge=nextedge; *in_nextleaf=nextleaf; } /* addnextleaf */ /******************/ /* free memory (to be called after inittree) */ void freetree_orig(ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc) /* No. of species */ { int i; for (i = 0; i < 2 * Maxspc - 3; i++) free(edge[i].edgemap); free(edge); free(edgeofleaf); } /* freetree */ /******************/ /* writes OTU sitting on edge ed */ void writeOTU_orig(FILE *outfp, /* output file */ int ed, /* edge to subtree */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *column, /* current screen depth */ int *trueID) /* species permutation */ { int i; /* test whether we are on a leaf */ if (edge[ed].downright == NULL && edge[ed].downleft == NULL) { for (i = 1; i < nextleaf; i++) { if (edgeofleaf[i] == ed) { /* i is the leaf of ed */ *column += fputid(outfp, trueID[i]); return; } } } /* we are NOT on a leaf */ fprintf(outfp, "("); (*column)++; writeOTU_orig(outfp, edge[ed].downleft->numedge, edge, edgeofleaf, nextedge, nextleaf, column, trueID); fprintf(outfp, ","); (*column)++; (*column)++; if (*column > 55) { *column = 2; fprintf(outfp, "\n "); } writeOTU_orig(outfp, edge[ed].downright->numedge, edge, edgeofleaf, nextedge, nextleaf, column, trueID); fprintf(outfp, ")"); (*column)++; } /* writeOTU */ /******************/ /* write tree */ void writetree_orig(FILE *outfp, /* output file */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *trueID) /* species permutation */ { int column; column = 1; fprintf(outfp, "("); column += fputid(outfp, trueID[0]) + 3; fprintf(outfp, ","); writeOTU_orig(outfp, edge[edgeofleaf[0]].downleft->numedge, edge, edgeofleaf, nextedge, nextleaf, &column, trueID); column++; column++; fprintf(outfp, ","); writeOTU_orig(outfp, edge[edgeofleaf[0]].downright->numedge, edge, edgeofleaf, nextedge, nextleaf, &column, trueID); fprintf(outfp, ");\n"); } /* writetree */ /******************/ /* clear all edgeinfos */ void resetedgeinfo_orig(ONEEDGE_ORIG *edge, /* edge array */ int nextedge) /* next free edge idx */ { int i; for (i = 0; i < nextedge; i++) edge[i].edgeinfo = 0; } /* resetedgeinfo */ /******************/ /* increment all edgeinfo between leaf A and B */ void incrementedgeinfo_orig(int A, /* start leaf of penalty path */ int B, /* start leaf of penalty path */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf) /* ext. edge idx array */ { int curredge, finaledge, nextstep; if (A == B) return; finaledge = edgeofleaf[B]; curredge = edgeofleaf[A]; edge[curredge].edgeinfo = edge[curredge].edgeinfo + 1; while (curredge != finaledge) { nextstep = (edge[curredge].edgemap)[finaledge]; switch (nextstep) { /* up */ case 1: curredge = (edge[curredge].up)->numedge; break; /* up/down left */ case 2: curredge = ((edge[curredge].up)->downleft)->numedge; break; /* up/down right */ case 3: curredge = ((edge[curredge].up)->downright)->numedge; break; /* down left */ case 4: curredge = (edge[curredge].downleft)->numedge; break; /* down right */ case 5: curredge = (edge[curredge].downright)->numedge; break; } edge[curredge].edgeinfo = edge[curredge].edgeinfo + 1; } } /* incrementedgeinfo */ /******************/ /* checks which edge has the lowest edgeinfo if there are several edges with the same lowest edgeinfo, one of them will be selected randomly */ void minimumedgeinfo_orig(ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *out_minedge, /* minimum edge set */ uli *out_mininfo) /* minumum penalty */ { int i, k, howmany, randomnum; int minedge; /* minimum edge set */ uli mininfo; /* minumum penalty */ howmany = 1; minedge = 0; mininfo = edge[0].edgeinfo; for (i = 1; i < nextedge; i++) if (edge[i].edgeinfo <= mininfo) { if (edge[i].edgeinfo == mininfo) { howmany++; } else { minedge = i; mininfo = edge[i].edgeinfo; howmany = 1; } } if (howmany > 1) { /* draw random edge */ randomnum = randominteger(howmany) + 1; /* 1 to howmany */ i = -1; for (k = 0; k < randomnum; k++) { do { i++; } while (edge[i].edgeinfo != mininfo); minedge = i; } } *out_minedge=minedge; *out_mininfo=mininfo; } /* minimumedgeinfo */ /*************************************************************************/ /* global functions of the puzzling step */ /*************************************************************************/ /* perform one single puzzling step to produce one intermediate tree */ void onepstep( /* PStep (intermediate) tree topol: */ ONEEDGE_ORIG **edge, /* out: new array of edges */ int **edgeofleaf, /* out: array of extern edge ptrs */ unsigned char *quartettopols, /* in: quartetblock with all topols */ int Maxspc, /* in: Number of species (n) */ ivector permutation) /* in: species permutation (trueID) */ { int Maxbrnch = (2*Maxspc)-3; /* Number of branches (2n-3) */ int nextedge; /* next free edge index (=3) */ int nextleaf; /* next free leaf index (=3) */ int minedge; /* insertion edge of minimum penalty */ uli mininfo; /* minimum penalty */ int a, b, c, i; /* quartet leaves, i to be inserted */ int chooseX, chooseY; /* end leaves of penalty path */ /* allocate and initialize new tree topology */ inittree_orig(edge, edgeofleaf, Maxspc, Maxbrnch, &nextedge, &nextleaf); /* adding all other leafs */ for (i = 3; i < Maxspc; i++) { /* clear all edgeinfos */ resetedgeinfo_orig(*edge, nextedge); /* * core of quartet puzzling algorithm */ for (a = 0; a < nextleaf - 2; a++) for (b = a + 1; b < nextleaf - 1; b++) for (c = b + 1; c < nextleaf; c++) { /* check which two leaves out of a,b,c are closer related to each other than to leaf i according to a least squares fit of the continous Bayesian weights to the seven trivial "attractive regions". We assign a score of 1 to all edges on the penalty path between these two leaves chooseX and chooseY */ checkquartet(a, b, c, i, permutation, &chooseX, &chooseY); incrementedgeinfo_orig(chooseX, chooseY, *edge, *edgeofleaf); } /* for all quartets q=(a,b,c,i) */ /* find out which edge has lowest edgeinfo */ minimumedgeinfo_orig(*edge, *edgeofleaf, nextedge, nextleaf, &minedge, &mininfo); /* add the next leaf on minedge */ addnextleaf_orig(minedge, *edge, *edgeofleaf, Maxspc, Maxbrnch, &nextedge, &nextleaf); } /* adding all other leafs */ } /* onepstep */ /*************************************************************************/ /* perform Numtrial single puzzling steps constructing Numtrial intermediate */ /* trees, sort each of them and extract splits for consensus step */ void allpstep(uli Numtrial, /* in: no. psteps to perform */ unsigned char *quartetinfo, /* in: quartetblock with all topols*/ int Maxspc, /* in: Number of species (n) */ int fixedorder_optn) /* in: 'fixed' anchored RNG (debug)*/ { /* misc variables */ ivector trueIDtmp; /* species permutation (trueID) */ uli Currtrial; /* step counter */ /* PStep (intermediate) tree topol: */ ONEEDGE_ORIG *tmpedgeset; /* array of edges */ int *tmpedgeofleaf; /* array of extern edge pointers */ /* for unique sorting of tree topologies */ int *ctree; /* sort tree */ int startnode; /* root in sort tree */ char *trstr; /* phylip tree string */ treelistitemtype *treeitem; /* list entry of tree */ # if PARALLEL cmatrix *bp; /* temporary buffer for splits in slaves */ int n; /* step count for init/free split buffer */ # endif /* PARALLEL */ # if PARALLEL /* add times to arry */ addtimes(GENERAL, &tarr); /* alloc temporary split memory */ bp = (cmatrix *) calloc((size_t) Numtrial, sizeof(void *)); for(n=0; n phylip tree string */ trstr=sprintfctree(ctree, psteptreestrlen); /* add sorted tree to unique tree list */ treeitem = addtree2list(&trstr, 1, &psteptreelist, &psteptreenum, &psteptreesum); # if ! PARALLEL /* output unique tree to trace list, if option set */ /* not done on slave processes */ if((listqptrees == PSTOUT_LIST) || (listqptrees == PSTOUT_LISTORDER)) { /* print: order no/# topol per this id/tree id/sum of unique topologies/sum of trees so far */ fprintf(qptlist, "%ld.\t1\t%d\t%d\t%d\t%d\n", Currtrial + 1, (*treeitem).count, (*treeitem).id, psteptreenum, psteptreesum); } # endif /* ! PARALLEL */ # ifdef VERBOSE1 printf("%s\n", trstr); printfsortedpstrees(psteptreelist); # endif /* free sorting tree structure */ freectree(&ctree); /* free tree before building the next tree */ freetree_orig(tmpedgeset, tmpedgeofleaf, Maxspc); # if ! PARALLEL /* generate message roughly every 15 minutes */ /* check timer */ time(&time2); if ( (time2 - time1) > TIMECHECK_INTERVAL) { double tc2, mintogo, minutes, hours; /* every TIMECHECK_INTERVAL seconds */ /* percentage of completed trees */ if (mflag == 0) { fprintf(STDOUT, "\n"); mflag = 1; } tc2 = 100.0*Currtrial/Numtrial; /* excluded for less runtime, but less accuracy of the 15min */ /* + 100.0*nq/Numquartets/Numtrial; */ mintogo = (100.0-tc2) * (double) (time2-time0)/60.0/tc2; hours = floor(mintogo/60.0); minutes = mintogo - 60.0*hours; fprintf(STDOUT, "%2.2f%%", tc2); fprintf(STDOUT, " completed (remaining"); fprintf(STDOUT, " time: %.0f", hours); fprintf(STDOUT, " hours %.0f", minutes); fprintf(STDOUT, " minutes)\n"); fflush(STDOUT); time1 = time2; } /* check timer */ # endif /* ! PARALLEL */ addtimes(PUZZLING, &tarr); } /* for Numtrials */ # if PARALLEL /* in slaves: send results: splits, trees */ PP_SendSplitsBlock(Maxspc, Numtrial, bp, psteptreenum, psteptreelist); /* free temporary split memory */ for (Currtrial = 0; Currtrial < Numtrial; Currtrial++) { free_cmatrix(bp[Currtrial]); } free(bp); /* sent! Thus, in slave process not needed any more */ freetreelist(&psteptreelist, &psteptreenum, &psteptreesum); # endif /* PARALLEL */ } /* allpstep */ tree-puzzle-5.2/src/pstep-mrca.h0000644000076400001440000001517410073365434012357 /* * pstep-mrca.h * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifndef PSTEP_ORIG_H #define PSTEP_ORIG_H #include #include #include"puzzle.h" #include"util.h" /* #include"newpstep.h" */ #ifndef ONEEDGE # define ONEEDGE ONEEDGE_ORIG #endif /* ! ONEEDGE_DEFINED */ /* tree structure */ typedef struct oneedge_orig { /* pointer to other three edges */ struct oneedge_orig *up; struct oneedge_orig *downleft; struct oneedge_orig *downright; int numedge; /* number of edge (index) */ uli edgeinfo; /* value of this edge (penalty) */ int *edgemap; /* pointer to the local edgemap array */ } ONEEDGE_ORIG; /*****************************************************************************/ /* internal functions for representing and building puzzling step trees */ /*****************************************************************************/ /* initialize tree with the following starting configuration * * 2 * 0 +------- C(=2) * A(=0) -----+ * +------- B(=1) * 1 * * * A(=0) * [up =NULL] * [downleft =1] * [downright=2] * * o * | * | * +-------------+--------------+ * | | * | | * o o * * C(=1) B(=2) * [up =0] [up =0] * [downleft =NULL] [downleft =NULL] * [downright=NULL] [downright=NULL] * * nextedge = 3 * nextleaf = 3 * and set according edge maps * */ void inittree_orig(ONEEDGE_ORIG **edge, /* out: new array of edges */ int **edgeofleaf,/* out: array of external edge ptrs */ int Maxspc, /* in: Number of species (n) */ int Maxbrnch, /* in: Number of branches (2n-3) */ int *nextedge, /* out: next free edge index (=3) */ int *nextleaf); /* out: next free leaf index (=3) */ /* add next leaf on the specified edge */ void addnextleaf_orig(int dockedge, /* insert here */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc, /* No. of species */ int Maxbrnch, /* No. of branches */ int *nextedge, /* next free edge idx */ int *nextleaf); /* next free leaf idx */ /* free memory (to be called after inittree) */ void freetree_orig(ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc); /* No. of species */ /* writes OTU sitting on edge ed */ void writeOTU_orig(FILE *outfp, /* output file */ int ed, /* edge to subtree */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *column, /* current screen depth */ int *trueID); /* species permutation */ /* write tree */ void writetree_orig(FILE *outfp, /* output file */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *trueID); /* species permutation */ /* clear all edgeinfos */ void resetedgeinfo_orig(ONEEDGE_ORIG *edge, /* edge array */ int nextedge); /* next free edge idx */ /* increment all edgeinfo between leaf A and B */ void incrementedgeinfo_orig(int A, /* start leaf of penalty path */ int B, /* start leaf of penalty path */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf); /* ext. edge idx array */ /* checks which edge has the lowest edgeinfo if there are several edges with the same lowest edgeinfo, one of them will be selected randomly */ void minimumedgeinfo_orig(ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *minedge, /* minimum edge set */ uli *mininfo); /* minumum penalty */ /*****************************************************************************/ /* global functions for representing and building puzzling step trees */ /*****************************************************************************/ /* perform one single puzzling step to produce one intermediate tree */ void onepstep( /* PStep (intermediate) tree topol: */ ONEEDGE_ORIG **edge, /* out: new array of edges */ int **edgeofleaf, /* out: array of extern edge ptrs */ unsigned char *quartettopols, /* in: quartetblock with all topols */ int Maxspc, /* in: Number of species (n) */ ivector permutation); /* in: species permutation (trueID) */ /* perform Numtrial single puzzling steps constructing Numtrial intermediate */ /* trees, sort each of them and extract splits for consensus step */ void allpstep(uli Numtrial, /* in: no. psteps to perform */ unsigned char *quartetinfo, /* in: quartetblock with all topols*/ int Maxspc, /* in: Number of species (n) */ int fixedorder_optn); /* in: 'fixed' anchored RNG (debug)*/ #endif /* PSTEP_ORIG_H */ tree-puzzle-5.2/src/pstep-orig.c0000644000076400001440000003036610073365437012373 /* * pstep-orig.c * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #define EXTERN extern #include #include #include"puzzle.h" /* #include"util.h" */ /* #include"pstep.h" */ #include /******************************************************************************/ /* functions for representing and building puzzling step trees */ /******************************************************************************/ /* initialize tree with the following starting configuration 2 0 +------- C(=2) A(=0) -----+ +------- B(=1) 1 */ void inittree() { int i; /* allocate the memory for the whole tree */ /* allocate memory for vector with all the edges of the tree */ edge = (ONEEDGE *) calloc((size_t) Maxbrnch, sizeof(ONEEDGE) ); if (edge == NULL) maerror("edge in inittree"); /* allocate memory for vector with edge numbers of leaves */ edgeofleaf = (int *) calloc((size_t) Maxspc, sizeof(int) ); if (edgeofleaf == NULL) maerror("edgeofleaf in inittree"); /* allocate memory for all the edges the edge map */ for (i = 0; i < Maxbrnch; i++) { edge[i].edgemap = (int *) calloc((size_t) Maxbrnch, sizeof(int) ); if (edge[i].edgemap == NULL) maerror("edgemap in inittree"); } /* number all edges */ for (i = 0; i < Maxbrnch; i++) edge[i].numedge = i; /* initialize tree */ nextedge = 3; nextleaf = 3; /* edge maps */ (edge[0].edgemap)[0] = 0; /* you are on the right edge */ (edge[0].edgemap)[1] = 4; /* go down left for leaf 1 */ (edge[0].edgemap)[2] = 5; /* go down right for leaf 2 */ (edge[1].edgemap)[0] = 1; /* go up for leaf 0 */ (edge[1].edgemap)[1] = 0; /* you are on the right edge */ (edge[1].edgemap)[2] = 3; /* go up/down right for leaf 2 */ (edge[2].edgemap)[0] = 1; /* go up for leaf 0 */ (edge[2].edgemap)[1] = 2; /* go up/down left for leaf 1 */ (edge[2].edgemap)[2] = 0; /* you are on the right edge */ /* interconnection */ edge[0].up = NULL; edge[0].downleft = &edge[1]; edge[0].downright = &edge[2]; edge[1].up = &edge[0]; edge[1].downleft = NULL; edge[1].downright = NULL; edge[2].up = &edge[0]; edge[2].downleft = NULL; edge[2].downright = NULL; /* edges of leaves */ edgeofleaf[0] = 0; edgeofleaf[1] = 1; edgeofleaf[2] = 2; } /* inittree */ /* add next leaf on the specified edge */ void addnextleaf(int dockedge) { int i; if (dockedge >= nextedge) { /* Trying to add leaf nextleaf to nonexisting edge dockedge */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR F TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } if (nextleaf >= Maxspc) { /* Trying to add leaf nextleaf to a tree with Maxspc leaves */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR G TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } /* necessary change in edgeofleaf if dockedge == edgeofleaf[0] */ if (edgeofleaf[0] == dockedge) edgeofleaf[0] = nextedge; /* adding nextedge to the tree */ edge[nextedge].up = edge[dockedge].up; edge[nextedge].downleft = &edge[dockedge]; edge[nextedge].downright = &edge[nextedge+1]; edge[dockedge].up = &edge[nextedge]; if (edge[nextedge].up != NULL) { if ( ((edge[nextedge].up)->downleft) == &edge[dockedge] ) (edge[nextedge].up)->downleft = &edge[nextedge]; else (edge[nextedge].up)->downright = &edge[nextedge]; } /* adding nextedge + 1 to the tree */ edge[nextedge+1].up = &edge[nextedge]; edge[nextedge+1].downleft = NULL; edge[nextedge+1].downright = NULL; edgeofleaf[nextleaf] = nextedge+1; /* the two new edges get info about the old edges */ /* nextedge */ for (i = 0; i < nextedge; i++) { switch ( (edge[dockedge].edgemap)[i] ) { /* down right changes to down left */ case 5: (edge[nextedge].edgemap)[i] = 4; break; /* null changes to down left */ case 0: (edge[nextedge].edgemap)[i] = 4; break; default: (edge[nextedge].edgemap)[i] = (edge[dockedge].edgemap)[i]; break; } } /* nextedge + 1 */ for (i = 0; i < nextedge; i++) { switch ( (edge[dockedge].edgemap)[i] ) { /* up/down left changes to up */ case 2: (edge[nextedge+1].edgemap)[i] = 1; break; /* up/down right changes to up */ case 3: (edge[nextedge+1].edgemap)[i] = 1; break; /* down left changes to up/down left */ case 4: (edge[nextedge+1].edgemap)[i] = 2; break; /* down right changes to up/down left */ case 5: (edge[nextedge+1].edgemap)[i] = 2; break; /* null changes to up/down left */ case 0: (edge[nextedge+1].edgemap)[i] = 2; break; /* up stays up */ default: (edge[nextedge+1].edgemap)[i] = (edge[dockedge].edgemap)[i]; break; } } /* dockedge */ for (i = 0; i < nextedge; i++) { switch ( (edge[dockedge].edgemap)[i] ) { /* up/down right changes to up */ case 3: (edge[dockedge].edgemap)[i] = 1; break; /* up/down left changes to up */ case 2: (edge[dockedge].edgemap)[i] = 1; break; default: break; } } /* all edgemaps are updated for the two new edges */ /* nextedge */ (edge[nextedge].edgemap)[nextedge] = 0; (edge[nextedge].edgemap)[nextedge+1] = 5; /* down right */ /* nextedge + 1 */ (edge[nextedge+1].edgemap)[nextedge] = 1; /* up */ (edge[nextedge+1].edgemap)[nextedge+1] = 0; /* all other edges */ for (i = 0; i < nextedge; i++) { (edge[i].edgemap)[nextedge] = (edge[i].edgemap)[dockedge]; (edge[i].edgemap)[nextedge+1] = (edge[i].edgemap)[dockedge]; } /* an extra for dockedge */ (edge[dockedge].edgemap)[nextedge] = 1; /* up */ (edge[dockedge].edgemap)[nextedge+1] = 3; /* up/down right */ nextleaf++; nextedge = nextedge + 2; } /* addnextleaf */ /* free memory (to be called after inittree) */ void freetree() { int i; for (i = 0; i < 2 * Maxspc - 3; i++) free(edge[i].edgemap); free(edge); free(edgeofleaf); } /* freetree */ /* writes OTU sitting on edge ed */ void writeOTU(FILE *outfp, int ed) { int i; /* test whether we are on a leaf */ if (edge[ed].downright == NULL && edge[ed].downleft == NULL) { for (i = 1; i < nextleaf; i++) { if (edgeofleaf[i] == ed) { /* i is the leaf of ed */ column += fputid(outfp, trueID[i]); return; } } } /* we are NOT on a leaf */ fprintf(outfp, "("); column++; writeOTU(outfp, edge[ed].downleft->numedge); fprintf(outfp, ","); column++; column++; if (column > 55) { column = 2; fprintf(outfp, "\n "); } writeOTU(outfp, edge[ed].downright->numedge); fprintf(outfp, ")"); column++; } /* writeOTU */ /* write tree */ void writetree(FILE *outfp) { column = 1; fprintf(outfp, "("); column += fputid(outfp, trueID[0]) + 3; fprintf(outfp, ","); writeOTU(outfp, edge[edgeofleaf[0]].downleft->numedge); column++; column++; fprintf(outfp, ","); writeOTU(outfp, edge[edgeofleaf[0]].downright->numedge); fprintf(outfp, ");\n"); } /* writetree */ /* clear all edgeinfos */ void resetedgeinfo() { int i; for (i = 0; i < nextedge; i++) edge[i].edgeinfo = 0; } /* resetedgeinfo */ /* increment all edgeinfo between leaf A and B */ void incrementedgeinfo(int A, int B) { int curredge, finaledge, nextstep; if (A == B) return; finaledge = edgeofleaf[B]; curredge = edgeofleaf[A]; edge[curredge].edgeinfo = edge[curredge].edgeinfo + 1; while (curredge != finaledge) { nextstep = (edge[curredge].edgemap)[finaledge]; switch (nextstep) { /* up */ case 1: curredge = (edge[curredge].up)->numedge; break; /* up/down left */ case 2: curredge = ((edge[curredge].up)->downleft)->numedge; break; /* up/down right */ case 3: curredge = ((edge[curredge].up)->downright)->numedge; break; /* down left */ case 4: curredge = (edge[curredge].downleft)->numedge; break; /* down right */ case 5: curredge = (edge[curredge].downright)->numedge; break; } edge[curredge].edgeinfo = edge[curredge].edgeinfo + 1; } } /* incrementedgeinfo */ /* checks which edge has the lowest edgeinfo if there are several edges with the same lowest edgeinfo, one of them will be selected randomly */ void minimumedgeinfo() { int i, k, howmany, randomnum; howmany = 1; minedge = 0; mininfo = edge[0].edgeinfo; for (i = 1; i < nextedge; i++) if (edge[i].edgeinfo <= mininfo) { if (edge[i].edgeinfo == mininfo) { howmany++; } else { minedge = i; mininfo = edge[i].edgeinfo; howmany = 1; } } if (howmany > 1) { /* draw random edge */ randomnum = randominteger(howmany) + 1; /* 1 to howmany */ i = -1; for (k = 0; k < randomnum; k++) { do { i++; } while (edge[i].edgeinfo != mininfo); minedge = i; } } } /* minimumedgeinfo */ tree-puzzle-5.2/src/pstep-orig.h0000644000076400001440000000465010073365443012372 /* * pstep-orig.h * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifndef PSTEP_ORIG_H #define PSTEP_ORIG_H #include #include #include"puzzle.h" #include"util.h" /* #include"newpstep.h" */ #include #ifndef ONEEDGE_DEFINED #define ONEEDGE_DEFINED /* tree structure */ typedef struct oneedge { /* pointer to other three edges */ struct oneedge *up; struct oneedge *downleft; struct oneedge *downright; int numedge; /* number of edge */ uli edgeinfo; /* value of this edge */ int *edgemap; /* pointer to the local edgemap */ } ONEEDGE; #endif /* ! ONEEDGE_DEFINED */ EXTERN int *edgeofleaf; /* vector with edge number of all leaves */ EXTERN int minedge; /* edge with minimum edgeinfo */ EXTERN int nextedge; /* number of edges in the current tree */ EXTERN int nextleaf; /* next leaf to add to tree */ EXTERN ONEEDGE *edge; /* vector with all the edges of the tree */ uli *splitcomp; /* bipartition storage */ uli *splitfreqs; /* frequencies of all different splits of all trees */ uli *splitpatterns; /* all different splits of all trees */ #if 0 EXTERN int Maxbrnch; /* 2*Maxspc - 3 */ EXTERN int Maxspc; /* Maxspc */ #endif ivector trueID; int column; uli mininfo; /* value of edgeinfo on minedge */ /*****************************************************************************/ /* functions for representing and building puzzling step trees */ /*****************************************************************************/ /* initialize tree with the following starting configuration * * 2 * 0 +------- C(=2) * A(=0) -----+ * +------- B(=1) * 1 */ void inittree(void); void addnextleaf(int); void freetree(void); void writeOTU(FILE *, int); void writetree(FILE *); void resetedgeinfo(void); void incrementedgeinfo(int, int); void minimumedgeinfo(void); #endif /* PSTEP_ORIG_H */ tree-puzzle-5.2/src/pstep-recursive.c0000644000076400001440000005270610073365450013437 /* * pstep-recursive.c * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifdef HAVE_CONFIG_H # include #endif #define EXTERN extern #include #include #include"puzzle.h" /* #include"util.h" */ /* #include"pstep.h" */ /******************************************************************************/ /* functions for representing and building puzzling step trees */ /******************************************************************************/ /* initialize tree with the following starting configuration * A(=0) * [up =NULL] * [downleft =1] * [downright=2] * * o * | * | * +-------------+--------------+ * | | * | | * o o * * C(=1) B(=2) * [up =0] [up =0] * [downleft =NULL] [downleft =NULL] * [downright=NULL] [downright=NULL] * * nextedge = 3 * nextleaf = 3 * and set according edge maps * */ void inittree_orig(ONEEDGE_ORIG **edge, /* out: new array of edges */ int **edgeofleaf,/* out: array of external edge ptrs */ int Maxspc, /* in: Number of species (n) */ int Maxbrnch, /* in: Number of branches (2n-3) */ int *nextedge, /* out: next free edge index (=3) */ int *nextleaf) /* out: next free leaf index (=3) */ { int i; ONEEDGE_ORIG *tmpedge; int *tmpedgeofleaf; /* allocate the memory for the whole tree */ /* allocate memory for vector with all the edges of the tree */ tmpedge = (ONEEDGE_ORIG *) calloc((size_t) Maxbrnch, sizeof(ONEEDGE_ORIG) ); if (tmpedge == NULL) maerror("edge in inittree"); *edge = tmpedge; /* allocate memory for vetmpctor with edge numbers of leaves */ tmpedgeofleaf = (int *) calloc((size_t) Maxspc, sizeof(int) ); if (tmpedgeofleaf == NULL) maerror("edgeofleaf in inittree"); *edgeofleaf = tmpedgeofleaf; /* allocate memory for all the edges the edge map */ for (i = 0; i < Maxbrnch; i++) { (tmpedge)[i].edgemap = (int *) calloc((size_t) Maxbrnch, sizeof(int) ); if (tmpedge[i].edgemap == NULL) maerror("edgemap in inittree"); } /* number all edges */ for (i = 0; i < Maxbrnch; i++) tmpedge[i].numedge = i; /* initialize tree */ *nextedge = 3; *nextleaf = 3; /* edge maps */ (tmpedge[0].edgemap)[0] = 0; /* you are on the right edge */ (tmpedge[0].edgemap)[1] = 4; /* go down left for leaf 1 */ (tmpedge[0].edgemap)[2] = 5; /* go down right for leaf 2 */ (tmpedge[1].edgemap)[0] = 1; /* go up for leaf 0 */ (tmpedge[1].edgemap)[1] = 0; /* you are on the right edge */ (tmpedge[1].edgemap)[2] = 3; /* go up/down right for leaf 2 */ (tmpedge[2].edgemap)[0] = 1; /* go up for leaf 0 */ (tmpedge[2].edgemap)[1] = 2; /* go up/down left for leaf 1 */ (tmpedge[2].edgemap)[2] = 0; /* you are on the right edge */ /* interconnection */ tmpedge[0].up = NULL; tmpedge[0].downleft = &tmpedge[1]; tmpedge[0].downright = &tmpedge[2]; tmpedge[1].up = &tmpedge[0]; tmpedge[1].downleft = NULL; tmpedge[1].downright = NULL; tmpedge[2].up = &tmpedge[0]; tmpedge[2].downleft = NULL; tmpedge[2].downright = NULL; /* edges of leaves */ tmpedgeofleaf[0] = 0; tmpedgeofleaf[1] = 1; tmpedgeofleaf[2] = 2; } /* inittree */ /******************/ /* add next leaf on the specified edge */ void addnextleaf_orig(int dockedge, /* insert here */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc, /* No. of species */ int Maxbrnch, /* No. of branches */ int *in_nextedge, /* next free edge idx */ int *in_nextleaf) /* next free leaf idx */ { int i; int nextedge; int nextleaf; nextedge=*in_nextedge; nextleaf=*in_nextleaf; if (dockedge >= nextedge) { /* Trying to add leaf nextleaf to nonexisting edge dockedge */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR F TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } if (nextleaf >= Maxspc) { /* Trying to add leaf nextleaf to a tree with Maxspc leaves */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR G TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } /* necessary change in edgeofleaf if dockedge == edgeofleaf[0] */ if (edgeofleaf[0] == dockedge) edgeofleaf[0] = nextedge; /* adding nextedge to the tree */ edge[nextedge].up = edge[dockedge].up; edge[nextedge].downleft = &edge[dockedge]; edge[nextedge].downright = &edge[nextedge+1]; edge[dockedge].up = &edge[nextedge]; if (edge[nextedge].up != NULL) { if ( ((edge[nextedge].up)->downleft) == &edge[dockedge] ) (edge[nextedge].up)->downleft = &edge[nextedge]; else (edge[nextedge].up)->downright = &edge[nextedge]; } /* adding nextedge + 1 to the tree */ edge[nextedge+1].up = &edge[nextedge]; edge[nextedge+1].downleft = NULL; edge[nextedge+1].downright = NULL; edgeofleaf[nextleaf] = nextedge+1; /* the two new edges get info about the old edges */ /* nextedge */ for (i = 0; i < nextedge; i++) { switch ( (edge[dockedge].edgemap)[i] ) { /* down right changes to down left */ case 5: (edge[nextedge].edgemap)[i] = 4; break; /* null changes to down left */ case 0: (edge[nextedge].edgemap)[i] = 4; break; default:(edge[nextedge].edgemap)[i] = (edge[dockedge].edgemap)[i]; break; } } /* nextedge + 1 */ for (i = 0; i < nextedge; i++) { switch ( (edge[dockedge].edgemap)[i] ) { /* up/down left changes to up */ case 2: (edge[nextedge+1].edgemap)[i] = 1; break; /* up/down right changes to up */ case 3: (edge[nextedge+1].edgemap)[i] = 1; break; /* down left changes to up/down left */ case 4: (edge[nextedge+1].edgemap)[i] = 2; break; /* down right changes to up/down left */ case 5: (edge[nextedge+1].edgemap)[i] = 2; break; /* null changes to up/down left */ case 0: (edge[nextedge+1].edgemap)[i] = 2; break; /* up stays up */ default:(edge[nextedge+1].edgemap)[i] = (edge[dockedge].edgemap)[i]; break; } } /* dockedge */ for (i = 0; i < nextedge; i++) { switch ( (edge[dockedge].edgemap)[i] ) { /* up/down right changes to up */ case 3: (edge[dockedge].edgemap)[i] = 1; break; /* up/down left changes to up */ case 2: (edge[dockedge].edgemap)[i] = 1; break; default: break; } } /* all edgemaps are updated for the two new edges */ /* nextedge */ (edge[nextedge].edgemap)[nextedge] = 0; (edge[nextedge].edgemap)[nextedge+1] = 5; /* down right */ /* nextedge + 1 */ (edge[nextedge+1].edgemap)[nextedge] = 1; /* up */ (edge[nextedge+1].edgemap)[nextedge+1] = 0; /* all other edges */ for (i = 0; i < nextedge; i++) { (edge[i].edgemap)[nextedge] = (edge[i].edgemap)[dockedge]; (edge[i].edgemap)[nextedge+1] = (edge[i].edgemap)[dockedge]; } /* an extra for dockedge */ (edge[dockedge].edgemap)[nextedge] = 1; /* up */ (edge[dockedge].edgemap)[nextedge+1] = 3; /* up/down right */ nextleaf++; nextedge = nextedge + 2; *in_nextedge=nextedge; *in_nextleaf=nextleaf; } /* addnextleaf */ /******************/ /* free memory (to be called after inittree) */ void freetree_orig(ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc) /* No. of species */ { int i; for (i = 0; i < 2 * Maxspc - 3; i++) free(edge[i].edgemap); free(edge); free(edgeofleaf); } /* freetree */ /******************/ /* writes OTU sitting on edge ed */ void writeOTU_orig(FILE *outfp, /* output file */ int ed, /* edge to subtree */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *column, /* current screen depth */ int *trueID) /* species permutation */ { int i; /* test whether we are on a leaf */ if (edge[ed].downright == NULL && edge[ed].downleft == NULL) { for (i = 1; i < nextleaf; i++) { if (edgeofleaf[i] == ed) { /* i is the leaf of ed */ *column += fputid(outfp, trueID[i]); return; } } } /* we are NOT on a leaf */ fprintf(outfp, "("); (*column)++; writeOTU_orig(outfp, edge[ed].downleft->numedge, edge, edgeofleaf, nextedge, nextleaf, column, trueID); fprintf(outfp, ","); (*column)++; (*column)++; if (*column > 55) { *column = 2; fprintf(outfp, "\n "); } writeOTU_orig(outfp, edge[ed].downright->numedge, edge, edgeofleaf, nextedge, nextleaf, column, trueID); fprintf(outfp, ")"); (*column)++; } /* writeOTU */ /******************/ /* write tree */ void writetree_orig(FILE *outfp, /* output file */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *trueID) /* species permutation */ { int column; column = 1; fprintf(outfp, "("); column += fputid(outfp, trueID[0]) + 3; fprintf(outfp, ","); writeOTU_orig(outfp, edge[edgeofleaf[0]].downleft->numedge, edge, edgeofleaf, nextedge, nextleaf, &column, trueID); column++; column++; fprintf(outfp, ","); writeOTU_orig(outfp, edge[edgeofleaf[0]].downright->numedge, edge, edgeofleaf, nextedge, nextleaf, &column, trueID); fprintf(outfp, ");\n"); } /* writetree */ /******************/ /* clear all edgeinfos */ void resetedgeinfo_orig(ONEEDGE_ORIG *edge, /* edge array */ int nextedge) /* next free edge idx */ { int i; for (i = 0; i < nextedge; i++) edge[i].edgeinfo = 0; } /* resetedgeinfo */ /******************/ /* increment all edgeinfo between leaf A and B */ void incrementedgeinfo_orig(int A, /* start leaf of penalty path */ int B, /* start leaf of penalty path */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf) /* ext. edge idx array */ { int curredge, finaledge, nextstep; if (A == B) return; finaledge = edgeofleaf[B]; curredge = edgeofleaf[A]; edge[curredge].edgeinfo = edge[curredge].edgeinfo + 1; while (curredge != finaledge) { nextstep = (edge[curredge].edgemap)[finaledge]; switch (nextstep) { /* up */ case 1: curredge = (edge[curredge].up)->numedge; break; /* up/down left */ case 2: curredge = ((edge[curredge].up)->downleft)->numedge; break; /* up/down right */ case 3: curredge = ((edge[curredge].up)->downright)->numedge; break; /* down left */ case 4: curredge = (edge[curredge].downleft)->numedge; break; /* down right */ case 5: curredge = (edge[curredge].downright)->numedge; break; } edge[curredge].edgeinfo = edge[curredge].edgeinfo + 1; } } /* incrementedgeinfo */ /******************/ /* checks which edge has the lowest edgeinfo if there are several edges with the same lowest edgeinfo, one of them will be selected randomly */ void minimumedgeinfo_orig(ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *out_minedge, /* minimum edge set */ uli *out_mininfo) /* minumum penalty */ { int i, k, howmany, randomnum; int minedge; /* minimum edge set */ uli mininfo; /* minumum penalty */ howmany = 1; minedge = 0; mininfo = edge[0].edgeinfo; for (i = 1; i < nextedge; i++) if (edge[i].edgeinfo <= mininfo) { if (edge[i].edgeinfo == mininfo) { howmany++; } else { minedge = i; mininfo = edge[i].edgeinfo; howmany = 1; } } if (howmany > 1) { /* draw random edge */ randomnum = randominteger(howmany) + 1; /* 1 to howmany */ i = -1; for (k = 0; k < randomnum; k++) { do { i++; } while (edge[i].edgeinfo != mininfo); minedge = i; } } *out_minedge=minedge; *out_mininfo=mininfo; } /* minimumedgeinfo */ /*************************************************************************/ /* global functions of the puzzling step */ /*************************************************************************/ /* perform one single puzzling step to produce one intermediate tree */ void onepstep( /* PStep (intermediate) tree topol: */ ONEEDGE_ORIG **edge, /* out: new array of edges */ int **edgeofleaf, /* out: array of extern edge ptrs */ unsigned char *quartettopols, /* in: quartetblock with all topols */ int Maxspc, /* in: Number of species (n) */ ivector permutation) /* in: species permutation (trueID) */ { int Maxbrnch = (2*Maxspc)-3; /* Number of branches (2n-3) */ int nextedge; /* next free edge index (=3) */ int nextleaf; /* next free leaf index (=3) */ int minedge; /* insertion edge of minimum penalty */ uli mininfo; /* minimum penalty */ int a, b, c, i; /* quartet leaves, i to be inserted */ int chooseX, chooseY; /* end leaves of penalty path */ /* allocate and initialize new tree topology */ inittree_orig(edge, edgeofleaf, Maxspc, Maxbrnch, &nextedge, &nextleaf); /* adding all other leafs */ for (i = 3; i < Maxspc; i++) { /* clear all edgeinfos */ resetedgeinfo_orig(*edge, nextedge); /* * core of quartet puzzling algorithm */ for (a = 0; a < nextleaf - 2; a++) for (b = a + 1; b < nextleaf - 1; b++) for (c = b + 1; c < nextleaf; c++) { /* check which two leaves out of a,b,c are closer related to each other than to leaf i according to a least squares fit of the continous Bayesian weights to the seven trivial "attractive regions". We assign a score of 1 to all edges on the penalty path between these two leaves chooseX and chooseY */ checkquartet(a, b, c, i, permutation, &chooseX, &chooseY); incrementedgeinfo_orig(chooseX, chooseY, *edge, *edgeofleaf); } /* for all quartets q=(a,b,c,i) */ /* find out which edge has lowest edgeinfo */ minimumedgeinfo_orig(*edge, *edgeofleaf, nextedge, nextleaf, &minedge, &mininfo); /* add the next leaf on minedge */ addnextleaf_orig(minedge, *edge, *edgeofleaf, Maxspc, Maxbrnch, &nextedge, &nextleaf); } /* adding all other leafs */ } /* onepstep */ /*************************************************************************/ /* perform Numtrial single puzzling steps constructing Numtrial intermediate */ /* trees, sort each of them and extract splits for consensus step */ void allpstep(uli Numtrial, /* in: no. psteps to perform */ unsigned char *quartetinfo, /* in: quartetblock with all topols*/ int Maxspc, /* in: Number of species (n) */ int fixedorder_optn) /* in: 'fixed' anchored RNG (debug)*/ { /* misc variables */ ivector trueIDtmp; /* species permutation (trueID) */ uli Currtrial; /* step counter */ /* PStep (intermediate) tree topol: */ ONEEDGE_ORIG *tmpedgeset; /* array of edges */ int *tmpedgeofleaf; /* array of extern edge pointers */ /* for unique sorting of tree topologies */ int *ctree; /* sort tree */ int startnode; /* root in sort tree */ char *trstr; /* phylip tree string */ treelistitemtype *treeitem; /* list entry of tree */ # if PARALLEL cmatrix *bp; /* temporary buffer for splits in slaves */ int n; /* step count for init/free split buffer */ # endif /* PARALLEL */ # if PARALLEL /* add times to arry */ addtimes(GENERAL, &tarr); /* alloc temporary split memory */ bp = (cmatrix *) calloc((size_t) Numtrial, sizeof(void *)); for(n=0; n phylip tree string */ trstr=sprintfctree(ctree, psteptreestrlen); /* add sorted tree to unique tree list */ treeitem = addtree2list(&trstr, 1, &psteptreelist, &psteptreenum, &psteptreesum); # if ! PARALLEL /* output unique tree to trace list, if option set */ /* not done on slave processes */ if((listqptrees == PSTOUT_LIST) || (listqptrees == PSTOUT_LISTORDER)) { /* print: order no/# topol per this id/tree id/sum of unique topologies/sum of trees so far */ fprintf(qptlist, "%ld.\t1\t%d\t%d\t%d\t%d\n", Currtrial + 1, (*treeitem).count, (*treeitem).id, psteptreenum, psteptreesum); } # endif /* ! PARALLEL */ # ifdef VERBOSE1 printf("%s\n", trstr); printfsortedpstrees(psteptreelist); # endif /* free sorting tree structure */ freectree(&ctree); /* free tree before building the next tree */ freetree_orig(tmpedgeset, tmpedgeofleaf, Maxspc); # if ! PARALLEL /* generate message roughly every 15 minutes */ /* check timer */ time(&time2); if ( (time2 - time1) > TIMECHECK_INTERVAL) { double tc2, mintogo, minutes, hours; /* every TIMECHECK_INTERVAL seconds */ /* percentage of completed trees */ if (mflag == 0) { fprintf(STDOUT, "\n"); mflag = 1; } tc2 = 100.0*Currtrial/Numtrial; /* excluded for less runtime, but less accuracy of the 15min */ /* + 100.0*nq/Numquartets/Numtrial; */ mintogo = (100.0-tc2) * (double) (time2-time0)/60.0/tc2; hours = floor(mintogo/60.0); minutes = mintogo - 60.0*hours; fprintf(STDOUT, "%2.2f%%", tc2); fprintf(STDOUT, " completed (remaining"); fprintf(STDOUT, " time: %.0f", hours); fprintf(STDOUT, " hours %.0f", minutes); fprintf(STDOUT, " minutes)\n"); fflush(STDOUT); time1 = time2; } /* check timer */ # endif /* ! PARALLEL */ addtimes(PUZZLING, &tarr); } /* for Numtrials */ # if PARALLEL /* in slaves: send results: splits, trees */ PP_SendSplitsBlock(Maxspc, Numtrial, bp, psteptreenum, psteptreelist); /* free temporary split memory */ for (Currtrial = 0; Currtrial < Numtrial; Currtrial++) { free_cmatrix(bp[Currtrial]); } free(bp); /* sent! Thus, in slave process not needed any more */ freetreelist(&psteptreelist, &psteptreenum, &psteptreesum); # endif /* PARALLEL */ } /* allpstep */ tree-puzzle-5.2/src/pstep-recursive.h0000644000076400001440000001520110073365455013436 /* * pstep-recursive.h * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifndef PSTEP_ORIG_H #define PSTEP_ORIG_H #include #include #include"puzzle.h" #include"util.h" /* #include"newpstep.h" */ #ifndef ONEEDGE # define ONEEDGE ONEEDGE_ORIG #endif /* ! ONEEDGE_DEFINED */ /* tree structure */ typedef struct oneedge_orig { /* pointer to other three edges */ struct oneedge_orig *up; struct oneedge_orig *downleft; struct oneedge_orig *downright; int numedge; /* number of edge (index) */ uli edgeinfo; /* value of this edge (penalty) */ int *edgemap; /* pointer to the local edgemap array */ } ONEEDGE_ORIG; /*****************************************************************************/ /* internal functions for representing and building puzzling step trees */ /*****************************************************************************/ /* initialize tree with the following starting configuration * * 2 * 0 +------- C(=2) * A(=0) -----+ * +------- B(=1) * 1 * * * A(=0) * [up =NULL] * [downleft =1] * [downright=2] * * o * | * | * +-------------+--------------+ * | | * | | * o o * * C(=1) B(=2) * [up =0] [up =0] * [downleft =NULL] [downleft =NULL] * [downright=NULL] [downright=NULL] * * nextedge = 3 * nextleaf = 3 * and set according edge maps * */ void inittree_orig(ONEEDGE_ORIG **edge, /* out: new array of edges */ int **edgeofleaf,/* out: array of external edge ptrs */ int Maxspc, /* in: Number of species (n) */ int Maxbrnch, /* in: Number of branches (2n-3) */ int *nextedge, /* out: next free edge index (=3) */ int *nextleaf); /* out: next free leaf index (=3) */ /* add next leaf on the specified edge */ void addnextleaf_orig(int dockedge, /* insert here */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc, /* No. of species */ int Maxbrnch, /* No. of branches */ int *nextedge, /* next free edge idx */ int *nextleaf); /* next free leaf idx */ /* free memory (to be called after inittree) */ void freetree_orig(ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc); /* No. of species */ /* writes OTU sitting on edge ed */ void writeOTU_orig(FILE *outfp, /* output file */ int ed, /* edge to subtree */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *column, /* current screen depth */ int *trueID); /* species permutation */ /* write tree */ void writetree_orig(FILE *outfp, /* output file */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *trueID); /* species permutation */ /* clear all edgeinfos */ void resetedgeinfo_orig(ONEEDGE_ORIG *edge, /* edge array */ int nextedge); /* next free edge idx */ /* increment all edgeinfo between leaf A and B */ void incrementedgeinfo_orig(int A, /* start leaf of penalty path */ int B, /* start leaf of penalty path */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf); /* ext. edge idx array */ /* checks which edge has the lowest edgeinfo if there are several edges with the same lowest edgeinfo, one of them will be selected randomly */ void minimumedgeinfo_orig(ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *minedge, /* minimum edge set */ uli *mininfo); /* minumum penalty */ /*****************************************************************************/ /* global functions for representing and building puzzling step trees */ /*****************************************************************************/ /* perform one single puzzling step to produce one intermediate tree */ void onepstep( /* PStep (intermediate) tree topol: */ ONEEDGE_ORIG **edge, /* out: new array of edges */ int **edgeofleaf, /* out: array of extern edge ptrs */ unsigned char *quartettopols, /* in: quartetblock with all topols */ int Maxspc, /* in: Number of species (n) */ ivector permutation); /* in: species permutation (trueID) */ /* perform Numtrial single puzzling steps constructing Numtrial intermediate */ /* trees, sort each of them and extract splits for consensus step */ void allpstep(uli Numtrial, /* in: no. psteps to perform */ unsigned char *quartetinfo, /* in: quartetblock with all topols*/ int Maxspc, /* in: Number of species (n) */ int fixedorder_optn); /* in: 'fixed' anchored RNG (debug)*/ #endif /* PSTEP_ORIG_H */ tree-puzzle-5.2/src/pstep-trueID.c0000644000076400001440000005402710073365462012625 /* * pstep-trueID.c (obsolete) * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifdef HAVE_CONFIG_H # include #endif #define EXTERN extern #include #include #include"puzzle.h" #if PARALLEL # include "ppuzzle.h" #endif /* #include"util.h" */ /* #include"pstep.h" */ /******************************************************************************/ /* functions for representing and building puzzling step trees */ /******************************************************************************/ /* initialize tree with the following starting configuration * A(=0) * [up =NULL] * [downleft =1] * [downright=2] * * o * | * | * +-------------+--------------+ * | | * | | * o o * * C(=1) B(=2) * [up =0] [up =0] * [downleft =NULL] [downleft =NULL] * [downright=NULL] [downright=NULL] * * nextedge = 3 * nextleaf = 3 * and set according edge maps * */ void inittree_orig(ONEEDGE_ORIG **edge, /* out: new array of edges */ int **edgeofleaf,/* out: array of external edge ptrs */ int Maxspc, /* in: Number of species (n) */ int Maxbrnch, /* in: Number of branches (2n-3) */ int *nextedge, /* out: next free edge index (=3) */ int *nextleaf) /* out: next free leaf index (=3) */ { int i; ONEEDGE_ORIG *tmpedge; int *tmpedgeofleaf; /* allocate the memory for the whole tree */ /* allocate memory for vector with all the edges of the tree */ tmpedge = (ONEEDGE_ORIG *) calloc((size_t) Maxbrnch, sizeof(ONEEDGE_ORIG) ); if (tmpedge == NULL) maerror("edge in inittree"); *edge = tmpedge; /* allocate memory for vetmpctor with edge numbers of leaves */ tmpedgeofleaf = (int *) calloc((size_t) Maxspc, sizeof(int) ); if (tmpedgeofleaf == NULL) maerror("edgeofleaf in inittree"); *edgeofleaf = tmpedgeofleaf; /* allocate memory for all the edges the edge map */ for (i = 0; i < Maxbrnch; i++) { (tmpedge)[i].edgemap = (int *) calloc((size_t) Maxbrnch, sizeof(int) ); if (tmpedge[i].edgemap == NULL) maerror("edgemap in inittree"); } /* number all edges */ for (i = 0; i < Maxbrnch; i++) tmpedge[i].numedge = i; /* initialize tree */ *nextedge = 3; *nextleaf = 3; /* edge maps */ (tmpedge[0].edgemap)[0] = 0; /* you are on the right edge */ (tmpedge[0].edgemap)[1] = 4; /* go down left for leaf 1 */ (tmpedge[0].edgemap)[2] = 5; /* go down right for leaf 2 */ (tmpedge[1].edgemap)[0] = 1; /* go up for leaf 0 */ (tmpedge[1].edgemap)[1] = 0; /* you are on the right edge */ (tmpedge[1].edgemap)[2] = 3; /* go up/down right for leaf 2 */ (tmpedge[2].edgemap)[0] = 1; /* go up for leaf 0 */ (tmpedge[2].edgemap)[1] = 2; /* go up/down left for leaf 1 */ (tmpedge[2].edgemap)[2] = 0; /* you are on the right edge */ /* interconnection */ tmpedge[0].up = NULL; tmpedge[0].downleft = &tmpedge[1]; tmpedge[0].downright = &tmpedge[2]; tmpedge[1].up = &tmpedge[0]; tmpedge[1].downleft = NULL; tmpedge[1].downright = NULL; tmpedge[2].up = &tmpedge[0]; tmpedge[2].downleft = NULL; tmpedge[2].downright = NULL; /* edges of leaves */ tmpedgeofleaf[0] = 0; tmpedgeofleaf[1] = 1; tmpedgeofleaf[2] = 2; } /* inittree */ /******************/ /* add next leaf on the specified edge */ void addnextleaf_orig(int dockedge, /* insert here */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc, /* No. of species */ int Maxbrnch, /* No. of branches */ int *in_nextedge, /* next free edge idx */ int *in_nextleaf) /* next free leaf idx */ { int i; int nextedge; int nextleaf; nextedge=*in_nextedge; nextleaf=*in_nextleaf; if (dockedge >= nextedge) { /* Trying to add leaf nextleaf to nonexisting edge dockedge */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR F TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } if (nextleaf >= Maxspc) { /* Trying to add leaf nextleaf to a tree with Maxspc leaves */ fprintf(STDOUT, "\n\n\nHALT: PLEASE REPORT ERROR G TO DEVELOPERS\n\n\n"); # if PARALLEL PP_Finalize(); # endif exit(1); } /* necessary change in edgeofleaf if dockedge == edgeofleaf[0] */ if (edgeofleaf[0] == dockedge) edgeofleaf[0] = nextedge; /* adding nextedge to the tree */ edge[nextedge].up = edge[dockedge].up; edge[nextedge].downleft = &edge[dockedge]; edge[nextedge].downright = &edge[nextedge+1]; edge[dockedge].up = &edge[nextedge]; if (edge[nextedge].up != NULL) { if ( ((edge[nextedge].up)->downleft) == &edge[dockedge] ) (edge[nextedge].up)->downleft = &edge[nextedge]; else (edge[nextedge].up)->downright = &edge[nextedge]; } /* adding nextedge + 1 to the tree */ edge[nextedge+1].up = &edge[nextedge]; edge[nextedge+1].downleft = NULL; edge[nextedge+1].downright = NULL; edgeofleaf[nextleaf] = nextedge+1; /* the two new edges get info about the old edges */ /* nextedge */ for (i = 0; i < nextedge; i++) { switch ( (edge[dockedge].edgemap)[i] ) { /* down right changes to down left */ case 5: (edge[nextedge].edgemap)[i] = 4; break; /* null changes to down left */ case 0: (edge[nextedge].edgemap)[i] = 4; break; default:(edge[nextedge].edgemap)[i] = (edge[dockedge].edgemap)[i]; break; } } /* nextedge + 1 */ for (i = 0; i < nextedge; i++) { switch ( (edge[dockedge].edgemap)[i] ) { /* up/down left changes to up */ case 2: (edge[nextedge+1].edgemap)[i] = 1; break; /* up/down right changes to up */ case 3: (edge[nextedge+1].edgemap)[i] = 1; break; /* down left changes to up/down left */ case 4: (edge[nextedge+1].edgemap)[i] = 2; break; /* down right changes to up/down left */ case 5: (edge[nextedge+1].edgemap)[i] = 2; break; /* null changes to up/down left */ case 0: (edge[nextedge+1].edgemap)[i] = 2; break; /* up stays up */ default:(edge[nextedge+1].edgemap)[i] = (edge[dockedge].edgemap)[i]; break; } } /* dockedge */ for (i = 0; i < nextedge; i++) { switch ( (edge[dockedge].edgemap)[i] ) { /* up/down right changes to up */ case 3: (edge[dockedge].edgemap)[i] = 1; break; /* up/down left changes to up */ case 2: (edge[dockedge].edgemap)[i] = 1; break; default: break; } } /* all edgemaps are updated for the two new edges */ /* nextedge */ (edge[nextedge].edgemap)[nextedge] = 0; (edge[nextedge].edgemap)[nextedge+1] = 5; /* down right */ /* nextedge + 1 */ (edge[nextedge+1].edgemap)[nextedge] = 1; /* up */ (edge[nextedge+1].edgemap)[nextedge+1] = 0; /* all other edges */ for (i = 0; i < nextedge; i++) { (edge[i].edgemap)[nextedge] = (edge[i].edgemap)[dockedge]; (edge[i].edgemap)[nextedge+1] = (edge[i].edgemap)[dockedge]; } /* an extra for dockedge */ (edge[dockedge].edgemap)[nextedge] = 1; /* up */ (edge[dockedge].edgemap)[nextedge+1] = 3; /* up/down right */ nextleaf++; nextedge = nextedge + 2; *in_nextedge=nextedge; *in_nextleaf=nextleaf; } /* addnextleaf */ /******************/ /* free memory (to be called after inittree) */ void freetree_orig(ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc) /* No. of species */ { int i; for (i = 0; i < 2 * Maxspc - 3; i++) free(edge[i].edgemap); free(edge); free(edgeofleaf); } /* freetree */ /******************/ /* trueID (HAS) */ /* writes OTU sitting on edge ed */ void writeOTU_orig(FILE *outfp, /* output file */ int ed, /* edge to subtree */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *column, /* current screen depth */ int *trueID) /* species permutation */ { int i; /* test whether we are on a leaf */ if (edge[ed].downright == NULL && edge[ed].downleft == NULL) { for (i = 1; i < nextleaf; i++) { if (edgeofleaf[i] == ed) { /* i is the leaf of ed */ *column += fputid(outfp, trueID[i]); return; } } } /* we are NOT on a leaf */ fprintf(outfp, "("); (*column)++; /* trueID (HAS) */ writeOTU_orig(outfp, edge[ed].downleft->numedge, edge, edgeofleaf, nextedge, nextleaf, column, trueID); fprintf(outfp, ","); (*column)++; (*column)++; if (*column > 55) { *column = 2; fprintf(outfp, "\n "); } /* trueID (HAS) */ writeOTU_orig(outfp, edge[ed].downright->numedge, edge, edgeofleaf, nextedge, nextleaf, column, trueID); fprintf(outfp, ")"); (*column)++; } /* writeOTU */ /******************/ /* trueID (HAS) */ /* write tree */ void writetree_orig(FILE *outfp, /* output file */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *trueID) /* species permutation */ { int column; column = 1; fprintf(outfp, "("); column += fputid(outfp, trueID[0]) + 3; fprintf(outfp, ","); /* trueID (HAS) */ writeOTU_orig(outfp, edge[edgeofleaf[0]].downleft->numedge, edge, edgeofleaf, nextedge, nextleaf, &column, trueID); column++; column++; fprintf(outfp, ","); /* trueID (HAS) */ writeOTU_orig(outfp, edge[edgeofleaf[0]].downright->numedge, edge, edgeofleaf, nextedge, nextleaf, &column, trueID); fprintf(outfp, ");\n"); } /* writetree */ /******************/ /* clear all edgeinfos */ void resetedgeinfo_orig(ONEEDGE_ORIG *edge, /* edge array */ int nextedge) /* next free edge idx */ { int i; for (i = 0; i < nextedge; i++) edge[i].edgeinfo = 0; } /* resetedgeinfo */ /******************/ /* increment all edgeinfo between leaf A and B */ void incrementedgeinfo_orig(int A, /* start leaf of penalty path */ int B, /* start leaf of penalty path */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf) /* ext. edge idx array */ { int curredge, finaledge, nextstep; if (A == B) return; finaledge = edgeofleaf[B]; curredge = edgeofleaf[A]; edge[curredge].edgeinfo = edge[curredge].edgeinfo + 1; while (curredge != finaledge) { nextstep = (edge[curredge].edgemap)[finaledge]; switch (nextstep) { /* up */ case 1: curredge = (edge[curredge].up)->numedge; break; /* up/down left */ case 2: curredge = ((edge[curredge].up)->downleft)->numedge; break; /* up/down right */ case 3: curredge = ((edge[curredge].up)->downright)->numedge; break; /* down left */ case 4: curredge = (edge[curredge].downleft)->numedge; break; /* down right */ case 5: curredge = (edge[curredge].downright)->numedge; break; } edge[curredge].edgeinfo = edge[curredge].edgeinfo + 1; } } /* incrementedgeinfo */ /******************/ /* checks which edge has the lowest edgeinfo if there are several edges with the same lowest edgeinfo, one of them will be selected randomly */ void minimumedgeinfo_orig(ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *out_minedge, /* minimum edge set */ uli *out_mininfo) /* minumum penalty */ { int i, k, howmany, randomnum; int minedge; /* minimum edge set */ uli mininfo; /* minumum penalty */ howmany = 1; minedge = 0; mininfo = edge[0].edgeinfo; for (i = 1; i < nextedge; i++) if (edge[i].edgeinfo <= mininfo) { if (edge[i].edgeinfo == mininfo) { howmany++; } else { minedge = i; mininfo = edge[i].edgeinfo; howmany = 1; } } if (howmany > 1) { /* draw random edge */ randomnum = randominteger(howmany) + 1; /* 1 to howmany */ i = -1; for (k = 0; k < randomnum; k++) { do { i++; } while (edge[i].edgeinfo != mininfo); minedge = i; } } *out_minedge=minedge; *out_mininfo=mininfo; } /* minimumedgeinfo */ /*************************************************************************/ /* global functions of the puzzling step */ /*************************************************************************/ /* trueID (HAS) */ /* perform one single puzzling step to produce one intermediate tree */ void onepstep( /* PStep (intermediate) tree topol: */ ONEEDGE_ORIG **edge, /* out: new array of edges */ int **edgeofleaf, /* out: array of extern edge ptrs */ unsigned char *quartettopols, /* in: quartetblock with all topols */ int Maxspc, /* in: Number of species (n) */ ivector permutation) /* in: species permutation (trueID) */ { int Maxbrnch = (2*Maxspc)-3; /* Number of branches (2n-3) */ int nextedge; /* next free edge index (=3) */ int nextleaf; /* next free leaf index (=3) */ int minedge; /* insertion edge of minimum penalty */ uli mininfo; /* minimum penalty */ int a, b, c, i; /* quartet leaves, i to be inserted */ int chooseX, chooseY; /* end leaves of penalty path */ /* allocate and initialize new tree topology */ inittree_orig(edge, edgeofleaf, Maxspc, Maxbrnch, &nextedge, &nextleaf); /* adding all other leafs */ for (i = 3; i < Maxspc; i++) { /* clear all edgeinfos */ resetedgeinfo_orig(*edge, nextedge); /* * core of quartet puzzling algorithm */ for (a = 0; a < nextleaf - 2; a++) for (b = a + 1; b < nextleaf - 1; b++) for (c = b + 1; c < nextleaf; c++) { /* check which two leaves out of a,b,c are closer related to each other than to leaf i according to a least squares fit of the continous Bayesian weights to the seven trivial "attractive regions". We assign a score of 1 to all edges on the penalty path between these two leaves chooseX and chooseY */ /* trueID (HAS) */ checkquartet_trueID(a, b, c, i, permutation, &chooseX, &chooseY); incrementedgeinfo_orig(chooseX, chooseY, *edge, *edgeofleaf); } /* for all quartets q=(a,b,c,i) */ /* find out which edge has lowest edgeinfo */ minimumedgeinfo_orig(*edge, *edgeofleaf, nextedge, nextleaf, &minedge, &mininfo); /* add the next leaf on minedge */ addnextleaf_orig(minedge, *edge, *edgeofleaf, Maxspc, Maxbrnch, &nextedge, &nextleaf); } /* adding all other leafs */ } /* onepstep */ /*************************************************************************/ /* perform Numtrial single puzzling steps constructing Numtrial intermediate */ /* trees, sort each of them and extract splits for consensus step */ void allpstep(uli Numtrial, /* in: no. psteps to perform */ unsigned char *quartetinfo, /* in: quartetblock with all topols*/ int Maxspc, /* in: Number of species (n) */ int fixedorder_optn) /* in: 'fixed' anchored RNG (debug)*/ { /* misc variables */ ivector trueIDtmp; /* species permutation (trueID) */ uli Currtrial; /* step counter */ /* PStep (intermediate) tree topol: */ ONEEDGE_ORIG *tmpedgeset; /* array of edges */ int *tmpedgeofleaf; /* array of extern edge pointers */ /* for unique sorting of tree topologies */ int *ctree; /* sort tree */ int startnode; /* root in sort tree */ char *trstr; /* phylip tree string */ treelistitemtype *treeitem; /* list entry of tree */ # if PARALLEL cmatrix *bp; /* temporary buffer for splits in slaves */ int n; /* step count for init/free split buffer */ # endif /* PARALLEL */ # if PARALLEL /* add times to arry */ addtimes(GENERAL, &tarr); /* alloc temporary split memory */ bp = (cmatrix *) calloc((size_t) Numtrial, sizeof(void *)); for(n=0; n phylip tree string */ trstr=sprintfctree(ctree, psteptreestrlen); /* add sorted tree to unique tree list */ treeitem = addtree2list(&trstr, 1, &psteptreelist, &psteptreenum, &psteptreesum); # if ! PARALLEL /* output unique tree to trace list, if option set */ /* not done on slave processes */ if((listqptrees == PSTOUT_LIST) || (listqptrees == PSTOUT_LISTORDER)) { /* print: order no/# topol per this id/tree id/sum of unique topologies/sum of trees so far */ fprintf(qptlist, "%ld.\t1\t%d\t%d\t%d\t%d\n", Currtrial + 1, (*treeitem).count, (*treeitem).id, psteptreenum, psteptreesum); } # endif /* ! PARALLEL */ # ifdef VERBOSE1 printf("%s\n", trstr); printfsortedpstrees(psteptreelist); # endif /* free sorting tree structure */ freectree(&ctree); /* free tree before building the next tree */ freetree_orig(tmpedgeset, tmpedgeofleaf, Maxspc); # if ! PARALLEL /* generate message roughly every 15 minutes */ /* check timer */ time(&time2); if ( (time2 - time1) > TIMECHECK_INTERVAL) { double tc2, mintogo, minutes, hours; /* every TIMECHECK_INTERVAL seconds */ /* percentage of completed trees */ if (mflag == 0) { fprintf(STDOUT, "\n"); mflag = 1; } tc2 = 100.0*Currtrial/Numtrial; /* excluded for less runtime, but less accuracy of the 15min */ /* + 100.0*nq/Numquartets/Numtrial; */ mintogo = (100.0-tc2) * (double) (time2-time0)/60.0/tc2; hours = floor(mintogo/60.0); minutes = mintogo - 60.0*hours; fprintf(STDOUT, "%2.2f%%", tc2); fprintf(STDOUT, " completed (remaining"); fprintf(STDOUT, " time: %.0f", hours); fprintf(STDOUT, " hours %.0f", minutes); fprintf(STDOUT, " minutes)\n"); fflush(STDOUT); time1 = time2; } /* check timer */ # endif /* ! PARALLEL */ addtimes(PUZZLING, &tarr); } /* for Numtrials */ # if PARALLEL /* in slaves: send results: splits, trees */ PP_SendSplitsBlock(Maxspc, Numtrial, bp, psteptreenum, psteptreelist); /* free temporary split memory */ for (Currtrial = 0; Currtrial < Numtrial; Currtrial++) { free_cmatrix(bp[Currtrial]); } free(bp); /* sent! Thus, in slave process not needed any more */ freetreelist(&psteptreelist, &psteptreenum, &psteptreesum); # endif /* PARALLEL */ } /* allpstep */ tree-puzzle-5.2/src/pstep-trueID.h0000644000076400001440000001521110073365466012626 /* * pstep-trueID.h (obsolete) * * * Part of TREE-PUZZLE 5.2 (July 2004) * * (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler * (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, * M. Vingron, and Arndt von Haeseler * (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler * * All parts of the source except where indicated are distributed under * the GNU public licence. See http://www.opensource.org for details. * * ($Id$) * */ #ifndef PSTEP_ORIG_H #define PSTEP_ORIG_H #include #include #include"puzzle.h" #include"util.h" /* #include"newpstep.h" */ #ifndef ONEEDGE # define ONEEDGE ONEEDGE_ORIG #endif /* ! ONEEDGE_DEFINED */ /* tree structure */ typedef struct oneedge_orig { /* pointer to other three edges */ struct oneedge_orig *up; struct oneedge_orig *downleft; struct oneedge_orig *downright; int numedge; /* number of edge (index) */ uli edgeinfo; /* value of this edge (penalty) */ int *edgemap; /* pointer to the local edgemap array */ } ONEEDGE_ORIG; /*****************************************************************************/ /* internal functions for representing and building puzzling step trees */ /*****************************************************************************/ /* initialize tree with the following starting configuration * * 2 * 0 +------- C(=2) * A(=0) -----+ * +------- B(=1) * 1 * * * A(=0) * [up =NULL] * [downleft =1] * [downright=2] * * o * | * | * +-------------+--------------+ * | | * | | * o o * * C(=1) B(=2) * [up =0] [up =0] * [downleft =NULL] [downleft =NULL] * [downright=NULL] [downright=NULL] * * nextedge = 3 * nextleaf = 3 * and set according edge maps * */ void inittree_orig(ONEEDGE_ORIG **edge, /* out: new array of edges */ int **edgeofleaf,/* out: array of external edge ptrs */ int Maxspc, /* in: Number of species (n) */ int Maxbrnch, /* in: Number of branches (2n-3) */ int *nextedge, /* out: next free edge index (=3) */ int *nextleaf); /* out: next free leaf index (=3) */ /* add next leaf on the specified edge */ void addnextleaf_orig(int dockedge, /* insert here */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc, /* No. of species */ int Maxbrnch, /* No. of branches */ int *nextedge, /* next free edge idx */ int *nextleaf); /* next free leaf idx */ /* free memory (to be called after inittree) */ void freetree_orig(ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int Maxspc); /* No. of species */ /* writes OTU sitting on edge ed */ void writeOTU_orig(FILE *outfp, /* output file */ int ed, /* edge to subtree */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *column, /* current screen depth */ int *trueID); /* species permutation */ /* write tree */ void writetree_orig(FILE *outfp, /* output file */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *trueID); /* species permutation */ /* clear all edgeinfos */ void resetedgeinfo_orig(ONEEDGE_ORIG *edge, /* edge array */ int nextedge); /* next free edge idx */ /* increment all edgeinfo between leaf A and B */ void incrementedgeinfo_orig(int A, /* start leaf of penalty path */ int B, /* start leaf of penalty path */ ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf); /* ext. edge idx array */ /* checks which edge has the lowest edgeinfo if there are several edges with the same lowest edgeinfo, one of them will be selected randomly */ void minimumedgeinfo_orig(ONEEDGE_ORIG *edge, /* edge array */ int *edgeofleaf, /* ext. edge idx array */ int nextedge, /* next free edge idx */ int nextleaf, /* next free leaf idx */ int *minedge, /* minimum edge set */ uli *mininfo); /* minumum penalty */ /*****************************************************************************/ /* global functions for representing and building puzzling step trees */ /*****************************************************************************/ /* perform one single puzzling step to produce one intermediate tree */ void onepstep( /* PStep (intermediate) tree topol: */ ONEEDGE_ORIG **edge, /* out: new array of edges */ int **edgeofleaf, /* out: array of extern edge ptrs */ unsigned char *quartettopols, /* in: quartetblock with all topols */ int Maxspc, /* in: Number of species (n) */ ivector permutation); /* in: species permutation (trueID) */ /* perform Numtrial single puzzling steps constructing Numtrial intermediate */ /* trees, sort each of them and extract splits for consensus step */ void allpstep(uli Numtrial, /* in: no. psteps to perform */ unsigned char *quartetinfo, /* in: quartetblock with all topols*/ int Maxspc, /* in: Number of species (n) */ int fixedorder_optn); /* in: 'fixed' anchored RNG (debug)*/ #endif /* PSTEP_ORIG_H */ tree-puzzle-5.2/NEWS0000644000076400001440000000000007147061652010024 tree-puzzle-5.2/data/0000777000076400001440000000000010075312110010312 5tree-puzzle-5.2/data/EF.phy0000644000076400001440000005047307560577342011304 22 915 EFTU_ECOLI--------------SKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLA EFTU_HELPY-------------MAKEKFNRTKPHVNIGTIGHVDHGKTTLSAAISAVLS EFTU_MYCGE-------------MAREKFDRSKPHVNVGTIGHIDHGKTTLTAAICTVLA EF1A_SULAC-------------------MSQKPHLNLIVIGHVDHGKSTLIGRLLMDRG EF1A_DESMO-----------------MSAPQKPHLNIVIIGHVDHGKSTMTGHILYRLG EF1A_AERPE-------------------MAEKPHMNLVVIGHVDHGKSTLVGHLLYRLG EF11_HUMAN------------------MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCG EF12_MOUSE------------------MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCG EF1A_CAEEL------------------MGKEKVHINIVVIGHVDSGKSTTTGHLIYKCG EF11_DAUCA------------------MGKEKVHINIVVIGHVDSGKSTTTGHLIYKLG EF1A_DICDI---------------MEFPESEKTHINIVVIGHVDAGKSTTTGHLIYKCG EF2_SULAC ------PRYKTVEQVLSLMKDVTRVRNIGIIAHVDHGKTTTSDTLLAASG EF2_AERPE ----MGARVKVVSEIEKIMRNIDQIRNIGIIAHVDHGKTTTSDSLLAAAG EF2_DESMO -----MVRFKQTSEVLKIMRNIEQIRNIGITAHVDHGKTTLSDSLLSAAG EF2_MOUSE -------VNFTVDQIRAIMDKKANIRNMSVIAHVDHGKSTLTDSLVCKAG EF2_HUMAN -------VNFTVDQIRAIMDKKANIRNMSVIAHVDHGKSTLTDSLVCKAG EF2_CAEEL -------VNFTVDEIRALMDRKRNIRNMSVIAHVDHGKSTLTDSLVSKAG EF2_DICDI ------MVNFTIDQIRAIMDRRENIRNMSVIAHVDHGKTTLSDSLIQRAG EF2_BETVU ------MVKFTADELRAIMDCKHNIRNMSVIAHVDHGKSTLTDSLVAAAG EFG_ECOLI ----------------ARTTPIARYRNIGISAHIDAGKTTTTERILFYTG EFG_HELPY ----------------ARKTPLNRIRNIGIAAHIDAGKTTTSERILFYTG EFG_MYCGE ---------------MSRTVDLKNFRNFGIMAHIDAGKTTTSERILFHSG KTY---------------GGAARAFDQIDNAPEEKARGITINTSHVEYDT LKG---------------LAEMKDYDNIDNAPEEKERGITIATSHIEYET KEG---------------KSAATRYDEIDKAPEEKARGITINSAHVEYSS FIDEKTVKEAEEAAKKLGKDSEKYAFLMDRLKEERERGVTINLSFMRFET YFDEKTVKMIEEESKKMGKESFKFAWLLDRMKEERERGVTISLSYMKFET YIEEKKLKELEEQAKSRGKESFKFAWILDKMKEERERGITIDLTFMKFET GIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERGITIDISLWKFET GIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERGITIDISLWKFET GIDKRTIEKFEKEAQEMGKGSFKYAWVLDKLKAERERGITIDIALWKFET GIDKRVIERFEKEAAEMNKRSFKYAWVLDKLKAERERGITIDIALWKFET GIDKRVIEKYEKEASEMGKQSFKYAWVMDKLKAERERGITIDIALWKFET IIS---------------QKVAGEALALDYLSVEQQRGITVKAANISLYH IIS---------------ERIAGEALVLDYLNVEKQRGITVKSANVSLYH LLS---------------EKIAGQALALDYLDVEQKRQMTVKAANASLYH IIA---------------SARAGETRFTDTRKDEQERCITIKSTAISLFY IIA---------------SARAGETRFTDTRKDEQERCITIKSTAISLFY IIA---------------GSKAGETRFTDTRKDEQERCITIKSTAISLFF IIA---------------DKVSGDMRYMSCRADEQERGITIKSSSVSLHF IIA---------------QEVAGDVRMTDTRADEAERGITIKSTGISLYY VNHKI-------------GEVHDGAATMDWMEQEQERGITITSAATTAFW VSHKI-------------GEVHDGAATMDWMEQEKERGITITSAATTCFW RIHKI-------------GETHDGESVMDWMEQEKERGITITSAATSVSW PT----------------------------RHYAHVDCPGHADYVKNMIT EN----------------------------RHYAHVDCPGHADYVKNMIT DK----------------------------RHYAHVDCPGHADYIKNMIT RK----------------------------YFFTVIDAPGHRDFVKNMIT KK----------------------------YFFTIIDAPGHRDFVKNMIT KK----------------------------YVFTIIDAPGHRDFVKNMIT SK----------------------------YYVTIIDAPGHRDFIKNMIT TK----------------------------YYITIIDAPGHRDFIKNMIT AK----------------------------YYITIIDAPGHRDFIKNMIT NK----------------------------YYCTVIDAPGHRDFIKNMIT SK----------------------------YYFTIIDAPGHRDFIKNMIT EIDGKG------------------------YVINLIDTPGHVDFSGRVTR EYEGKP------------------------YVINLIDTPGHVDFSGKVTR EYKGKP------------------------YLINLIDTPGHVDFQSKTIR ELSENDLNFIKQSK-------DG-----SGFLINLIDSPGHVDFSSEVTA ELSENDLNFIKQSK-------DG-----AGFLINLIDSPGHVDFSSEVTA ELEKKDLEFVKGENQFETVEVDGKKEKYNGFLINLIDSPGHVDFSSEVTA EMPKEDKLPAGCTS--------------HEFLINLIDSPGHVDFSSEVTA QMTDEALQSYKGER-------KG-----NDYLINLIDSPGHVDFSSEVTA SGMAKQYE---------------------PHRINIIDTPGHVDFTIEVER K----------------------------DHQINLIDTPGHVDFTIEVER K----------------------------NCSLNLIDTPGHVDFTVEVER GAAQMDGAILVVAATDG-------PMPQTREHILLGRQVG------VPYI GAAQMDGAILVVSAADG-------PMPQTREHILLSRQVG------VPHI GAAQMDGAILVVSATDS-------VMPQTREHILLARQVG------VPKM GASQADAAILVVSAKKGEYEAGMSAEGQTREHIILSKTMG------INQV GASQADAAILVVSARKGEFEAGMSAEGQTREHAILARTMG------INQL GASQADAAILVVSARKGEFEAGMSTEGQTREHLLLARTMG------IEQI GTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLAYTLG------VKQL GTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLAYTLG------VKQL GTSQADCAVLVVACGTGEFEAGISKNGQTREHALLAQTLG------VKQL GTSQADCAVLIIDPTTGGFEAGISKDGQTREHALLAFTLG------VKQM GTSQADCAVLVIASPTGEFEAGIAKNGQTREHALLAYTLG------VKQM SLRVLDGSIVVIDAVEGIMTQTETVLRQSLEGRVRPILFINKVDRLIKEL SLRVLDGAIVVVDAVEGVMTQTETVIRQALEERVRPILFINKVDRLIKEL ALRVIDGAIVVVDAVEGVMTQTEMYLRVALEERVRPVLFINKIDRLIKEL ALRVTDGALVVVDCVSGVCVQTETVLRQAIAERIKPVLMMNKMDRALLEL ALRVTDGALVVVDCVSGVCVQTETVLRQAIAERIKPVLMMNKMDRALLEL ALRVTDGALVVVDCVSGVCVQTETVLRQAIAERIKPVLFMNKMDRALLEL ALRVTDGALVVIDCVEGVCVQTETVLRQAVAERIKPVLFVNKVDRFLLEL ALRITDGALVVVDCIEGVCVQTETVLRQALGERIRPVLTVNKMDRCFLEL SMRVLDGAVMVYCAVGGVQPQSETVWRQANKYKVPRIAFVNKMDRMGANF SMRVLDGAVSVFCSVGGVQPQSETVWRQANKYGVPRIVFVNKMDRIGANF SLRVLDGAIAVLDAQMGVEPQTETVWRQASRYEVPRVIFVNKMDKTGANF IVFLNKCDMVD---DEELLELVEMEVR---ELLSQYDFPGDDTPIVRGSA VVFLNKQDMVD---DQELLELVEMEVR---ELLSAYEFPGDDTPIVAGSA VVFLNKCDIAS---DEEVQELVAEEVR---DLLTSYGFDGKNTPIIYGSA IVAINKMDLADTPYDEKRFKEIVDTVS---KFMKSFGFDMNKVKFVPVVA IVAINKMDATEPPYSEKRYNEIKEILG---KFLKGLGYDVSKIPFIPISA IVAVNKMDAPDVNYDQKRYEFVVSVLK---KFMKGLGYQVDKIPFIPVSA IVGVNKMDSTEPPYSQKRYEEIVKEVS---TYIKKIGYNPDTVAFVPISG IVGVNKMDSTEPAYSEKRYDEIVKEVS---AYIKKIGYNPATVPFVPISG IVACNKMDSTEPPFSEARFTEITNEVS---GFIKKIGYNPKAVPFVPISG ICCCNKMDATTPKYSKARYDEIVKEVS---SYLKKVGYNPEKIAFVPISG IVAINKMDEKSTNYSQARYDEIVKEVS---SFIKKIGYNPEKVAFVPISG KLSSQEIQKRLIDLIIEVNNLIETYGEP--EFKDQWKIKPELGNVVFGSA KLPPEKIQQRFVEIIKEVNNLIDLYAEP--EFRKKWKLDPNAGMVAFGSA R-SPNEIQQRLVQIVKDVNTLIATYADK--EFQKAWLLDPMKG-QAFGSA QLEPEELYQTFQRIVENVNVIISTYGEGESGPMGNIMIDPVLGTVGFGSG QLEPEELYQTFQRIVENVNVIISTYGEGESGPMGNIMIDPVLGTVGFGSG QLGAEELFQTFQRIVENINVIIATYGD-DDGPMGPIMVDPSIGNVGFGSG QLNTEEAYLSFRRAIESVNVIVGNTED---KEFGDVTVSPEKGTVAFGSG QVDGEEAYTTFQKVIENANVIMATYED---PLLGDVQVYPEKGTVAFSAG LKVVNQIKTRLGANPVPLQLAIGAEEHFTGVVDLVKMKAINWNDADQGVT YNVENQIKLRLKANPVPINIPIGAEDTFIGVIDLVQMKAIVWNNETMGAK ERSVLSIQQRLGVKAVPIQFPIGAENDFNGIIDIITKKAYFFDG-NKEEN LKALEGD----------AEWEAK--------------------------- LRALEEAKAG-----NVGEWGEK--------------------------- LKALEGD----------PKWEAK--------------------------- PDGDNVTHKS-----TKMPWYN---------------------------- WTGENLIERS-----PNMPWYN---------------------------- WKGDNLIERS-----PNMPWYN---------------------------- WNGDNMLEPS-----ANMPWFKGWKVT----------------------- WHGDNMLEPS-----PNMPWFKGWKVE----------------------- FNGDNMLEVS-----SNMPWFKGWAVE----------------------- FEGDNMIERS-----TNLDWYK---------------------------- WNGDNMLERS-----DKMEWYK---------------------------- KDKWGFSVP-----MAGKRGVK---------------------------- KDKWGISVP-----QVKKKGIT---------------------------- RDRWGLTIP-----LVQQKGIK---------------------------- LHGWAFTLKQFAEMYVAKFAAKGEGQLSAAERAKKVEDMMKKLWGDRYFD LHGWAFTLKQFAEMYVAKFAAKGEGQLGPAERAKKVEDMMKKLWGDRYFD LHGWAFTLKQFAEMYAGKFGVQ-------------VDKLMKNLWGDRFFD LHGWGFTLGRFAKLYAAKFGDP-------------EDKLMGRLWGDSYFD LHGWAFTLSNFAKMYASKFGVD-------------ESKMMERLWGENFFD FEYEDIPADMVELANEWHQNLIESAAE----------------------- YDVEEIPSDLLEKAKEYREKLVEAVAE----------------------- AIEKPIPEQYVDQVEKLYNNLVEEVAS----------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- ---------------------------------FSDVVNAYTSGDKAKIE ---------------------------------FREIIQAYEKG-KEAVA ---------------------------------FSDIVDVYTKG-KEAVA PANGKFSKSANSPDGKKLPRTFCQLILDPIFKVFDAIMNFRKEETAKLIE PANGKFSKSATSPEGKKLPRTFCQLILDPIFKVFDAIMNFKKEETAKLIE LKTKKWSSTQTD-ESK---RGFCQFVLDPIFMVFDAVMNIKKDKTAALVE ATAKKWTSNPQSADGKALPRAFCQFVLEPIYQLTRAIVDEDAVKLEKMMK PATKKWTTKNSG--NASCKRGFVQFCYEPIKQIIAACMNDQKDKLLAHVT --------------------------------ASEELMEKYLGGEELTEA --------------------------------QDEALMEKYLGGEELSIE --------------------------------LDDQLMADYLDGKPIEID -----------------------------ILELAGFLDSYIPEPERAI-- -----------------------------VLKLMAEVDAYIPTPERDT-- -----------------------------IHDLIKAVDEWIPTPTREV-- -----------------------------GPTLEELLDQLEI-PPKPV-- -----------------------------GPTLVEALDTLEV-PPKPI-- -----------------------------GPTLVEALDQLQP-PAKPV-- ----------------------RKDGNASGTTLLEALDCILP-PTRPT-- ----------------------RKEGNASGVSLLEALDTILP-PTRPT-- ----------------------RKEGNASGKTLLEALDSIIP-PQRPT-- -----------------------------GPTLLDALDQINE-PKRPS-- -----------------------------GPTLLEALDAIVE-PKRPH-- ELASKV---------------------PIHEALLDAVIKFVPNPRDSQKY ELSKKM---------------------PLHETLLDMVIKFVPNPREAQRY ELQKAA---------------------PLHEAILDMVVKYVPNPRDAQRY KLDIKLDSEDKDKEGKPLLKAVMRRWLPAGDALLQMITIHLPSPVTAQKY KLDIKLDSEDKDKEGKPLLKAVMRRWLPAGDALLQMITIHLPSPVTAQKY KLGIKLANDEKDLEGKPLMKVFMRKWLPAGDTMLQMIAFHLPSPVTAQKY TLQITLAPEDAEIKGKQLVKAVMRKFLPAADAILSMIVTHLPSPLVAQKY KLGIQMKTEEKDLMGRPLMKRVMQTWLPASSALLEMMIHHLPSPATAQRY EIKGALRQRVLNNEIILVTCG-SAFKNKGVQAMLDAVIDYLPSP-----V EIKKGIKAGCLNMSLVPMLCG-SSFKNKGVQTLLDAVIDYLPAP-----T AIKNAIRNGVIHCKFFPVLCG-SAFKNKGIKLLLDAVVDFLPSP-----V -----------------------DKPFLLPIEDVFSISGRG-TVVTGRVE -----------------------EKTFLMPVEDVFSIAGRG-TVVTGRIE -----------------------DKPFLLAIEDTMTITGRG-TVVTGRVE -----------------------DKPLRIPIQEVYSISGVG-VVPVGRIE -----------------------NKPLRIPIQDVYNISGIG-VVPVGRVE -----------------------DKPLRIPVQNVYSIPGAG-TVPVGRVE -----------------------DKPLRLPLQDVYKIGGIG-TVPVGRVE -----------------------DKPLRLPLQDVYKIGGIG-TVPVGRVE -----------------------DRPLRLPLQDVYKIGGIG-TVPVGRVE -----------------------DKPLRLPLQDVYKIGGIG-TVPVGRVE -----------------------DKPLRIPLQDVYKIGGIG-TVPVGRVE RIPKIWKGDLDSEIAKAMINADPNGPIVMMINDMKVDPHAG-LVATGRVF RIPKIWKGDINSEIGQAMLNADPDGPLVFFINDVRIE-KAG-LVATGRVF RIPKIWHGDLNHEAVKYMMEADPNGPLVMLVNDIRVDPHAG-LVATGRIY RCELLYEGPPDDEAAMGIKSCDPKGPLMMYISKMVPTSDKGRFYAFGRVF RCELLYEGPPDDEAAMGIKSCDPKGPLMMYISKMVPTSDKGRFYAFGRVF RMEMLYEGPHDDEAAVAIKTCDPNGPLMMYISKMVPTSDKGRFYAFGRVF RCANLYEGPMDDECAVAIQKCDPNGPLMMYVSKMVPTSDKGRFYAFGRVF RVENLYEGPMDDVYATAIRNCDPEGPLMLYVSKMIPASDKGRFFAFGRVF DVPAINGILDDGKDTPAERHASDDEPFSALAFKIATDPFVG-NLTFFRVY EVVDIKG-IDPKTEEEVFVKSSDDGEFAGLAFKIMTDPFVG-QLTFVRVY DVPPAKA--IDANNKEISIKASDDANFIGLAFKVATDPFVG-RLTFIRVY RGIIKVGEEVEIVGIK-----------ETQKSTCTGVEMFRKLLDEGRAG RGVVKVGDEVEIVGIR-----------PTQKTTVTGVEMFRKELEKGEAG RGELKVGQEVEIVGLK-----------PIRKAVVTGIEMFKKELDSAMAG SGVLKVGDKIVFMPVG-------------KIGEVRSIETHHTKIDKAEPG TGVLKVGDKLVFMPAG-------------LVAEVKTIETHHTKIEKAEPG TGVLRVGDKVVFMPPG-------------VVGEVRSIEMHYQQLQQAEPG TGVLKPGMVVTFAPVN-------------VTTEVKSVEMHHEALSEALPG TGILRPGMVVTFAPVN-------------ITTEVKSVEMHHEALSEALPG TGIIKPGMVVTFAPQN-------------VTTEVKSVEMHHESLPEAVPG TGTIKPGMVVTFGPSG-------------LTTEVKSVEMHHESLLEALPG TGIIKPGMVVTFAPAG-------------LSTEVKSVEMHHEQLPEARPG SGTLRAGEEVWLVNAKRQ---------QRILQVSLYMGAIRELAEEIPVG SGTLRSGEEVYLLNAGKK---------SRLLQVSIYMGPFREVTKEIPAG SGTLRAGEEVWLVNARVP---------QRVLQVSLYMGPYRELADEITAG SGVVSTGLKVRIMGPNYTPGKKEDLYLKPIQRTILMMGRYVEPIEDVPCG SGLVSTGLKVRIMGPNYTPGKKEDLYLKPIQRTILMMGRYVEPIEDVPCG SGKVATGMKARIQGPNYVPGKKEDLYEKTIQRTILMMGRFIEPIEDIPSG SGIIVPVKRSELWVSTYVPGKKDDLFLKSIQRTVLMMGRKTEQIEDCPCG AGKVSTGMKVRIMGPNYVPGEKKDLYVKNVQRTVIWMGKKQETVEDVPCG SGVVNSGDTVLNSVKAAR---------ERFGRIVQMHANKREEIKEVRAG RGKLESGSYVYNSTKDKK---------ERVGRLLKMHSNKREDIKEVYAG AGVLKSGSYVKNVRKNKK---------ERVSRLVKMHAQNRNEIDEIRAG ENVGVL--------------------------LRGIKREEIERGQVLAKP DNVGVL--------------------------LRGTKKEEVERGMVLCKP DNAGVL--------------------------LRGVERKEVERGQVLAKP DNIGFN--------------------------VRGVEKKDVKRGDVAGSV DNIGFN--------------------------VKGVEKKDIKRGDVAGSL DNIGFA--------------------------VRGVSKSDIKRGDVAGHL DNVGFN--------------------------VKNVSVKDVRRGNVAGDS DNVGFN--------------------------VKNVSVKDIRRGNVCGDS DNVGFN--------------------------VKNVSVKDIRRGSVCSDS DNVGFN--------------------------VKNVSVKDLKRGYVASNS DNVGFN--------------------------VKNVSVKEIKRGMVAGDS NIAAALGMDAARSGETGVDIRFKDSVLGSFEKLHYISEPVVTISVEPRNP NIGAVMGFEDVRAGETVVSLGYEE-NAAPFESLRYVSEPVVTIAVEPVKI NIAAALALEKARSGETVVAMKYKD-SMTPFEKLRMITESVVTVAIEPKNP NIVGLVGVDQFLVKTGTITT-FEH--AHNMRVMKFSVSPVVRVAVEAKNP NIVGLVGVDQFLVKTGTITT-FEH--AHNMRVMKFSVSPVVRVAVEAKNP NIAGLVGVDQYLVKGGTITT-YKD--AHNMRVMKFSVSPVVRVAVEAKNP NIVGLVGVDQFLVKSGTITT-SEV--AHNIRVMKFSVSPVVRVAVEPKNP NTVALVGLDQYITKNATLTN-EKESDAHPIRAMKFSVSPVVRVAVQCKVA DIAAAIGLKDVTTGDTLCDPDAP-----IILERMEFPEPVISIAVEPKTK EICAFVGLKDTLTGDTLCDEKNA-----VVLERMEFPEPVIHIAVEPKTK DICAVIGLKDTTTGETLTDDKLD-----VQLEAMQFAEPVISLAVEPKTK GTIKPHT----KFESEVYILSK--DEGGRHTPFFKGYRPQFYFRTTDVTG GSITPHK----KFEGEIYVLSK--EEGGRHTPFFTNYRPQFYVRTTDVTG GSIKPHK----KFKAEIYALKK--EEGGRHTGFLNGYRPQFYFRTTDVTG QNPPTVA---DEFTAQVIVIWHPTAVGVGYTPVLHVHTASIACRVSEITS DVPPTVA---DEFTARIMVMWHPTAIAVGYTPVIHVHTASVACRITEIIA DKPPTVA---EEFEARIFVIWHPSAITVGYTPVIHVHTASVSSRIIEIKA KNDPPME--AAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACKFAELKE KADPPQE--AAQFTSQVIILNHPGQISAGYSPVIDCHTAHIACKFAELKE KQDPAKE--ARTFHAQVIIMNHPGQISNGYTPVLDCHTAHIACKFNELKE KDDPAKG--AASFTSQVIIMNHPGQIGNGYAPVLDCHTSHIAVKFAELLT KNDPPQE--TEKFVAQVIVLNHPGQIHAGYSPVLDCHTAHIACKFTEIVD KDLTKMIDALRKLSIEDSNLVVKINEETGEYLLSGMGFLHLEVSLQLLKE QDLPKMIEALRKLTIEDPNLVVKINEETGEYLLSGMGPLHLEIALTMLRE QQLTKLVDALYKLHLEDPSLIVKINEETGEYLLSGVGTLHIEIALTLLKD ADLPKLVEGLKRLAKSDPMVQCII-EESGEHIIAGAGELHLEICLKDLEE ADLPKLVEGLKRLAKSDPMVQCII-EESGEHIIAGAGELHLEICLKDLEE ADLPKLVEGLKRLAKSDPMVQCIF-EESGEHIIAGAGELHLEICLKDLEE SDLPKLVEGLKRLAKSDPCVLCYS-EESGEHIVAGAGELHLEICLKDLAE SDLPKLVEGLKRLAKSDPMVVCSI-EESGEHIIAGAGELHLEICLKDLQD ADQEKMGLALGRLAKEDPSFRVWTDEESNQTIIAGMGELHLDIIVDRMKR ADQEKMGVALGKLAEEDPSFRVMTQEETGQTLIGGMGELHLEIIVDRLKR ADQEKMSIALSKLAEEDPTFKTFSDPETGQTIIAGMGELHLDILVDRMKR TIEL----PEG--------------------------------------- SITL----PEG--------------------------------------- SIAL----AEN--------------------------------------- RIDP----KTGKEAEKN--------------------------------- KIDP----RTGKEIEKN--------------------------------- KLDP----KTGQVVEQN--------------------------------- KIDR----RSGKKLEDG--------------------------------- KIDR----RSGKKLEDN--------------------------------- KVDR----RTGKKVEDF--------------------------------- KIDR----RSGKELEKE--------------------------------- KVDR----RTGAVVAKEGTA------------------------------ N-YG-LDVVTTPPIVVYR--ESIRNKS-QVFEGKSPNKHNKLYISVEPLN K-FG-VEVKASPPIVVYR--ETVRQQS-RVFEGKSPNKHNKLYISVEPLN L-YG-LEVVASPPVIVYR--ETVRESS-QVFEGKSPNKHNKFYISVAPLN DHAC-IPIKKSDPVVSYR--ETVSEESNVLCLSKSPNKHNRLYMKARPFP DHAC-IPIKKSDPVVSYR--ETVSEESNVLCLSKSPNKHNRLYMKARPFP DHAC-IPLKKSDPVVSYR--ETVQSESNQICLSKSPNKHNRLHCTAQPMP DHAG-IEIKTTDPVVSFR--ESV---------------------KASPIS DFMGGAEIIKSDPVVSFR--ETVLDRSVRTVMSKSPNKHNRLYMEARPME EFNV--EANVGKPQVAYR--ETIRQKVTDVEGKHAKQSGGRGQYGHVVID EFKV--EAEIGQPQVAFR--ETIRSSVS-KEHKYAKQSGGRGQYGHVFIK EFKV--EVNIGAPQVSFR--ETFKSTSE-VEGKYIKQSGGRGQYGHVKIR -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- NQTIDLIANG-TIKEDMDN----KEMAKILRDQAEWDYDEAKKIVAIDEN EETITLIQNG-AVTEDQDP----KDRARILADKAGWDYNEARKIWAIDEN EETLRLMSEG-IIVEDMDA----RERAKILREQAGWDADEARRIMAIDEN DGLAEDIDKG-EVSARQEL----KARARYLAEKYEWDVAEARKIWCFGPD DGLAEDIDKG-EVSARQEL----KQRARYLAEKYEWDVAEARKIWCFGPD DGLADDIEGG-TVNARDEF----KARAKILAEKYEYDVTEARKIWCFGPD MELQDLIEAGSDISSKDDP----KARANYLADNHEWDKNDAMNIWSFGPE EGLAEAIDEG-RIGPRDDP----KNRSKILAEEYGWDKDLAKKIWCFGPE MYPLEPGSNP---------------------------------------- LEPKEPGS------------------------------------------ FEP-NKDK------------------------------------------ ------VEMVMPGDNIKMVVTLIHPIAMDDGL------RFAIREGGRTVG ------VEMVMPGDNVKITVELISPVALELGT------KFAIREGGRTVG ------TEMVLPGDNASITVELIAPIACEKGS------KFSIREGGRTVG ------PQFIKAGDSAIVKFKPIKELVAEKFREFPALGRFAMRDMGKTVG ------PHFLKQGDIAIVKFKPIKPLVVEKYSDFQGLGRFAMRDMGKTIG ------PQFLKAGDAAIVRFKPVKPLVVEKFSEIPQLGRFAMRDMNRTVG ------PKFLKSGDAAIVDMVPGKPMCVESFSDYPPLGRFAVRDMRQTVA ------PKSLKSGDAAIVEMVPGKPMCVESFSQYPPLGRFAVRDMRQTVA ------PKFLKSGDAGIVELIPTKPLCVESFTDYAPLGRFAVRDMRQTVA ------PKFLKNGDAGMVKMLPTKPMVVETFAEYPPLGRFAVRVMRQTVA ------AVVLKNGDAAMVELTPSRPMCVESFTEYPPLGRFAVRDMRQTVA ---INVFIDATSGVQHLREIMDTLLQGFRLAMKEGPLAFEPVRGVKVVLH ---INVFVDKTAGVQYLREVKDTIIAGFRLALKEGPLAAEPVRGVKVVLH ---LNMLVDMTTGVQYLREIKDTVIQGFRLAMKEGPLAMEPVRGVKVVLH GTGPNILTDITKGVQYLNEIKDSVVAGFQWATKEGALCEENMRGVRFDVH GTGPNILTDITKGVQYLNEIKDSVVAGFQWATKEGALCEENMRGVRFDVH GTGPNLLMDVTKGVQYLNEIKDSVVAGFQWATREGVLSDENMRGVRFNVH GNGANLLVNVTKGVQYLNEIKDSFVGAFQWATKEGVVCDENMRGIRFNLY TTGPNMVVDMCKGVQYLNEIKDSVVAGFQWASKEGALAEENMRGICFEVC --KGYEFINDIKGGVIPGEYIPAVDKGIQEQLKAGPLAGYPVVDMGIRLH ---GYEFVNEISGGVIPKEYIPAVDKGIQEAMQNGVLAGYPVVDFKVTLY ---GFEFVDKIVGGRIPREYIKPVQTGLENAMNSGPLAGYPMIDIKATLF AGVVAKVLS----------------------------------------- AGVVSNIIE----------------------------------------- AGTVTEVLE----------------------------------------- VGVIIDVKPRKVEVK----------------------------------- IGQVLEIKPAQVNIKK---------------------------------- IGIVTDVKPAKVDIKAK--------------------------------- VGVIKAVDKKAAGAGKVTKSAQKAQKAK---------------------- VGVIKNVEKKSGGAGKVTKSAQKAQKAGK--------------------- VGVIKSVEKSDGSSGKVTKSAQKAAPKKK--------------------- VGVIKAVEKKDPTGAKVTKAAAKKGAK----------------------- VGVIKSTVKKAPGKAGDKKGAAAPSKKK---------------------- DAVVHEDPAHRGPAQLYPAVRNAIFAGILTSKPTLLEPLQKLDIRIPMEY DAVIHEDPVHRGPGQLYPAVRNAIWAGILDGRPTLLEPLQKLDIRAPMEY DAVVHEDPAHRGPAQIFPAVRNAIFAGFLTAKPTILEPILKLDIRTPMEY DVTLHADAIHRGGGQIIPTARRCLYASVLTAQPRLMEPIYLVEIQCPEQV DVTLHADAIHRGGGQIIPTARRCLYASVLTAQPRLMEPIYLVEIQCPEQV DVTLHADAIHRGGGQIIPTARRVFYASVLTAEPRLLEPVYLVEIQCPEAA DVTLHTDAIHRGGGQIIPTARRVLYAAELTASPTLLEPIYLVEITAPENA DVVLHTDAIHRGGGQIIPTARRVFYASQLTAKPRLLEPVYLVEIQAPENA FGSYHDVDSSE--LAFKLAASIAFKEGFKKAKPVLLEPIMKVEVETPEEN DGSYHDVDSSE--MAFKIAGSMAFKEASRAANPVLLEPMMKVEVEVPEEY DGSFHEVDSSE--MAFKIAASLALKEAGKQCNPVLLEPIMAIEVTVPEQY -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- LGNVTAVITRKRGKVINVVQT--GNVARVYAEIPVGESFELASELRASSA LSNITAVLTRKRGRIINVETT--GVMARIIAAIPVAESFDLAGELRSATA IGNISTVITKKRGKLIEVQQM--ETSARVIAEIPVSESFDIADMLRNVTA VGGIYGVLNRKRGHVFEESQVAGTPMFVVKAYLPVNESFGFTADLRSNTG VGGIYGVLNRKRGHVFEESQVAGTPMFVVKAYLPVNESFGFTADLRSNTG VGGIYGVLNRRRGHVFEESQVTGTPMFVVKAYLPVNESFGFTADLRSNTG IGGIYSVLNRRRGIVIGEERRIGSPLFSVKAHLPVLESLRFTADLRSHTA LGGIYSVLNQKRGHVFEEMQRPGTPLYNIKAYLPVVESFGFSSTLRASTS TGDVIGDLSRRRGMLKGQESE--VTGVKIHAEVPLSEMFGYATQLRSLTK MGDVIGDLNRRRGQINSMDDR--LGLKIVNAFVPLVEMFGYSTDLRSATQ FGDTMGDISSRRGIIEGTEQR--DNVQLIKAKVPLKEMFGYATDLRSFSQ -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- GRAFWGTEFSRWAPVP------DSILVDLIMKIRERKGKPKQLPKVEDFI GRAFWGVEFYGWAPVP------DQMLQDLIAKIRQRKGLPPSPPKIDDLI GKAIWGQEFSRWAPVP------ESMLMDLVSKIRTRKGLKPEPPKLEDFL GQAFPQCVFDHWQILPGDPFDNSSRPSQVVAETRKRKGLKEGIPALDNFL GQAFPQCVFDHWQILPGDPFDNSSRPSQVVAETRKRKGLKEGIPALDNFL GQAFPQCVFDHWQVLPGDPLEAGTKPNQIVLDTRKRKGLKEGVPALDNYL GQAFPQCVFDHWASIG--VVNKDKKATEVALATRKRKGLAPEIPALDKFH GQAFPQCVFDHWEMMPSDPLEAGSQASTLVSVIRKRKGLKEQMTPLSEFE GRASYTMEFLKYDEAP------SNVAQAVIEARGK--------------- GRGTYSMEFDHYGEVP------SNIAKEIVEKRKG--------------- GRGNYVMQFSHYAETP------KSVVNEIIANKK---------------- --------------- --------------- --------------- --------------- --------------- --------------- --------------- --------------- --------------- --------------- --------------- S-------------- GP------------- SP------------- DKL------------ DKL------------ DKM------------ RKTINNLSHTLSFQI DKL------------ --------------- --------------- --------------- tree-puzzle-5.2/data/primates.trees0000644000076400001440000000014407642374753013150 (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); tree-puzzle-5.2/data/EF.3trees0000644000076400001440000000504107560577342011700 [tree - ((B2,(E2,C2)),(B1a,(E1a,C1a))) ] [ lh=-18965.865869 ](EFG_MYCGE:0.35044,(((((EF1A_SULAC:0.27436,EF1A_DESMO:0.15452)98:0.06186, EF1A_AERPE:0.19726)100:0.16339,((EF11_DAUCA:0.19788,EF1A_DICDI:0.17054) 68:0.08680,(EF11_HUMAN:0.04646,EF12_MOUSE:0.04777)64:0.06487,EF1A_CAEEL:0.12845) 88:0.47056)100:0.66538,((EFTU_ECOLI:0.16964,EFTU_HELPY:0.21648)100:0.10227, EFTU_MYCGE:0.22380)100:0.82551)100:2.71210,(((((EF2_MOUSE:0.00532, EF2_HUMAN:0.00411)100:0.11711,EF2_CAEEL:0.10100)98:0.13112,EF2_DICDI:0.32291) 94:0.08935,EF2_BETVU:0.22108)100:0.79422,((EF2_SULAC:0.22098,EF2_DESMO:0.26389) 100:0.06212,EF2_AERPE:0.15059)100:0.23638)99:0.48379)100:1.02287, (EFG_ECOLI:0.28597,EFG_HELPY:0.19713)99:0.14542); [tree2 - ((E2,(B2,C2)),(E1a,(B1a,C1a))) ] ( ( [E+2] ( ( ( ( EF2_HUMAN, EF2_MOUSE ), EF2_CAEEL ), EF2_DICDI ), EF2_BETVU ) [E-2] , ( [B+2] ( EFG_MYCGE, ( EFG_ECOLI, EFG_HELPY ) ) [B-2] , [A+2] ( EF2_AERPE, ( EF2_DESMO, EF2_SULAC ) ) [A-2] ) ) ,[root] ( [E+1a] ( ( EF11_HUMAN, EF12_MOUSE ), EF1A_CAEEL, ( EF11_DAUCA, EF1A_DICDI ) ) [E-1a] , ( [B+1a] ( ( EFTU_ECOLI, EFTU_HELPY ), EFTU_MYCGE ) [B-1a] , [A+1a] ( ( EF1A_DESMO, EF1A_SULAC ), EF1A_AERPE ) [A-1a] ) ) ) ; [tree3 - ((C2,(E2,B2)),(C1a,(E1a,B1a))) ] ( ( [A+2] ( EF2_AERPE, ( EF2_DESMO, EF2_SULAC ) ) [A-2] , ( [E+2] ( ( ( ( EF2_HUMAN, EF2_MOUSE ), EF2_CAEEL ), EF2_DICDI ), EF2_BETVU ) [E-2] , [B+2] ( EFG_MYCGE, ( EFG_ECOLI, EFG_HELPY ) ) [B-2] ) ), [root] ( [A+1a] ( ( EF1A_DESMO, EF1A_SULAC ), EF1A_AERPE ) [A-1a] , ( [E+1a] ( ( EF11_HUMAN, EF12_MOUSE ), EF1A_CAEEL, ( EF11_DAUCA, EF1A_DICDI ) ) [E-1a] , [B+1a] ( ( EFTU_ECOLI, EFTU_HELPY ), EFTU_MYCGE ) [B-1a] ) ) ) ; tree-puzzle-5.2/data/globin.a0000644000076400001440000000264407446451756011704 7 128 HBB_HUMAN HLTPEEKSAV TALWGKVNVD EVGGEALGRL LVVYPWTQRF FESFDLSMGN HBB_HORSE QLSGEEKAAV LALWDKVNEE EVGGEALGRL LVVYPWTQRF FDSFDLSMGN HBA_HUMAN VLSPADKTNV KAAWGKVGAG EYGAEALERM FLSFPTTKTY FPHFDLSHGS HBA_HORSE VLSAADKTNV KAAWSKVGAG EYGAEALERM FLGFPTTKTY FPHFDLSHGS MYG_PHYCA VLSEGEWQLV LHVWAKVEVA GHGQDILIRL FKSHPETLEK FDRFHLKKAS GLB5_PETMA PLSAAEKTKI RSAWAPVYYE TSGVDILVKF FTSTPAAQEF FPKFGLTKKS LGB2_LUPLU ALTESQAALV KSSWEEFNIP KHTHRFFILV LEIAPAAKDL FSFLGTSQNN PKVKAHGKKV LGAFSDGLAH LDNLKGTFAT LSELHCDKLH VDENFRLLGN PKVKAHGKKV LHSFGEGVHH LDNLKGTFAA LSELHCDKLH VDENFRLLGN AQVKGHGKKV ADALTNAVAH VDDMPNALSA LSDLHAHKLR VDVNFKLLSH AQVKAHGKKV GDALTLAVGH LDDLPGALSN LSDLHAHKLR VDVNFKLLSH EDLKKHGVTV LTALGAILKK KGHHEAELKP LAQSHATKHK IPKYLEFISE ADVRWHAERI INAVNDAVAS MDKMSMKLRD LSGKHAKSFQ VDQYFKVLAA PELQAHAGKV FKLVYEAAIQ LQVTDATLKN LGSVHVSKGV ADAHFPVVKE VLVCVLAHHQ AAYQKVVAGV ANALAHKY VLVVVLARHQ ASYQKVVAGV ANALAHKY CLLVTLAAHH ASLDKFLASV STVLTSKY CLLSTLAVHH ASLDKFLSSV STVLTSKY AIIHVLHSRQ GAMNKALELF RKDIAAKY VIADTVAAGD AGFEKLMSMI CILLRSAY AILKTIKEVN SAWTIAYDEL AIVIKKEM CLUSTAL W example "globin.pep" (kindly provided by Desmond Higgins). This file is part of the TREE-PUZZLE distribution. ($Id$) tree-puzzle-5.2/data/atp6.a0000644000076400001440000000457107446451716011301 7 226 chicken MNLSFFDQFS SPCLLGIPLI LPSLLLPALL LPSPNRWINN RLSTIQLWFT cat MNENLFASFT TPTMMGLPIV ILIIMFPSIL FPSPNRLINN RLVSLQQWLV horse MNENLFASFA TPTMVGLPIV ILIIMFPSIL FPSPNRLINN RLISIQQWLV mouse MNENLFASFI TPTMMGFPIV VAIIMFPSIL FPSSKRLINN RLHSFQHWLV opossum MNENLFAPFI TPTILGITTL PIIITFPCLI LSSPKRWLPN RIQILQMWLI platypus MNENLFAPFI TPTVLGISVL PLIMIFPCLL FSTSNRWVPN RLIALQLWLV rat MNENLFASFI TPTMMGLPIV VTIIMFPSIL FPSSERLISN RLHSFQHWLI HLITKQLMTP LNKAGHKWAL LLTSLILMLL SINLLGLLPY TFTPTTQLSM QLTSKQMLAI HNHKGQTWAL MLMSLILFIG STNLLGLLPH SFTPTTQLSM QLTSKQMMAI HNSKGQTWTL MLMSLILFIG STNLLGLLPH SFTPTTQLSM KLIIKQMMLI HTPKGRTWTL MIVSLIMFIG STNLLGLLPH TFTPTTQLSM RLITKQMMTM HNKQGRTWTL MLMSLILFIA STNLLGLLPY SFTPTTQLSM RLITKQMMMM HNKQGRMWTL MLITLIIFIA STNLLGLLPY TFTPTTQLSM KLIIKQMMLI HTPKGRTWAL MIVSLIMFIG STNLLGLLPH TFTPTTQLSM NMALALPLWL ATLLTGLRNQ PSASLGHLLP EGTPTPLIPA LIMIETTSLL NLGMAIPLWA GTVITGFRHK TKASLAHFLP QGTPVPLIPM LVVIETISLF NLGMAIPLWA GTVFMGFRHK TKAALAHFLP QGTPIFLIPM LVIIETISLF NLSMAIPLWA GAVITGFRHK LKSSLAHFLP QGTPISLIPM LIIIETISLF NIGMAIPLWA GTVIMGFRNK PKMSLAHFLP QGTPTPLIPM LIIIETISLF NMGMAIPLWM GTVLMGFRNK PKASLAHFLP QGTPTPLIPM LIIIETISLF DLSMAIPLWA GAVILGFRHK LKNSLAHFSP QGTPISLIPM LIIIETISLF IRPLALGVRL TANLTAGHLL IQLISTATIA LLPMMPSISA LTALILFLLT IQPMALAVRL TANITAGHLL MHLIGGAALA LMNISTSIAL ITFTILILLT IQPVALAVRL TANITAGHLL MHLIGGATLA LMSISPSTAL ITFIILILLT IQPMALAVRL TANITAGHLL MHLIGGATLV LMNISPPTAT ITFIILLLLT IQPLALAVRL TANITAGHLL IHLIGSATLA LSSISMTVST ITFSILFLLT IQPLALAVRL TANITAGHLL IHLIGSATLA LSSISLTVST ITFTILFLLT IQPMALAVRL TANITAGHLL MHLIGGATLV LMDISPPTAT ITFIILLLLT ILEVAVAMIQ AYVFVLLLSL YLQENI ILEFAVALIQ AYVFTLLVSL YLHDNT ILEFAVAMIQ AYVFTLLVSL YLHDNT ILEFAVALIQ AYVFTLLVSL YLHDNT LLEIAVAMIQ AYVFTLLVSL YLHDNS ILEFAVALIQ AYVFTLLVSL YLHDNT VLEFAVALIQ AYVFTLLVSL YLHDNT Mitochondrial ATP6 amino acid sequences from six mammals with chicken as outgroup. This file is part of the TREE-PUZZLE distribution. ($Id$) tree-puzzle-5.2/data/primates.b0000644000076400001440000001340107446452060012235 5 895 Gibbon 0001111010 0010100110 1111101001 1011101000 1100111111 1111011011 Human 0001111011 0010100110 1111101001 1011101000 1110101111 1011011011 Chimpanzee 0001111011 0010100110 1111101001 1011101000 1110101111 1011011011 Gorilla 0001111011 0010100110 1111101001 1011101000 1110101101 1011011011 Orangutan 0001111011 0010100110 1111101001 1011101000 1110101111 1111011011 1101111010 0011100011 0100010001 1101001101 0110100111 1011110000 1101110010 0011100011 0100010101 1101001101 0110100111 1111110000 1101110010 0011100011 0100010101 1101001101 0110100111 1111110000 1101110010 0011100011 0100010001 1101001101 0110100111 1111110000 1101110010 0011100011 0100010001 1101001101 0110100111 1111110000 0111100011 1101111101 1001001111 1100100111 0100100011 1101100111 0111100011 1101111101 1001001111 1100100111 1100100011 1101100111 0111100011 1101111101 1001001111 1100100111 1100100011 1101100111 0111100011 1101111101 1001001111 1100100111 1100100011 1101100111 1111100011 1101111111 1001001111 1100100111 1100100011 1101100111 1011110111 1110110110 0111111000 1000111111 0101100100 1111111111 1011110111 1110110110 0111011000 0000111111 0101100100 1101011111 1011110111 1110110110 0111111000 0000111111 0101100100 1111011111 1011110111 1110110110 0111011000 0000111111 0101100100 1101011111 1011110110 1110110110 0111111000 0000111111 0101100100 1101011111 1100010001 0110110110 1011101100 0111001010 1100110100 1111010111 1100110001 0110111111 1011101000 0111001010 1100110100 1111010111 1100110001 0110111111 1011101000 0111001010 1100110100 1111010111 1100110001 0110111111 1011101000 0111001010 1100110100 1111010111 1100111001 0110110111 1011001000 0111001010 1100110100 1111010111 1111101010 1110110100 1010010000 1010111010 1011010110 0000101000 1111101010 1110110100 1010010000 1110111011 1011010110 0100101000 1111101010 1110110100 1010010000 1110111011 1011010110 0100101000 1111101010 1110110100 1010010000 1110111010 1011010110 1100101000 1111101010 1110110100 1010010000 1010111010 1011010110 0100101000 0111110111 0101000000 0101011001 0111010101 1111111111 1111111111 0111110111 0101000000 0101111101 0111010101 1101111110 1111111111 0111110111 0101000000 0101111101 0111110101 1101111110 1111111111 0111110111 0101000000 0101111101 0111010101 1101111110 1111111111 0111111111 0101010000 0101111101 0111010101 1101111110 1111111111 0011111001 1110010110 1101100111 1011111101 0001010011 1001100001 0111111001 1110010110 1101100011 1111111101 0001010011 1001100001 0111111001 1110010110 1101100011 1011111101 0001010011 1001100001 0111111001 1110010110 1101100011 1011111101 0001010011 1001100001 0111111001 1110010110 1101100011 1011101101 0001010011 1001100001 0110001101 0001110010 0100000111 0000111111 0111011000 0000111010 0110001101 0001110010 0100000111 0100111111 0111011000 0000111010 0110001101 0001110010 0100000111 0100111111 0111011000 0000111010 0110001101 0001110010 0100000111 0100111111 0111011000 0000111010 0110001101 0001110010 0100001111 0100111111 0111011000 0000111010 0000110110 0111011011 1010101001 0010100111 1111001111 1000000100 0000110110 0111010111 1010111001 0010100111 1111001111 1000000100 0000110110 0111010111 1010111001 0010100111 1111001111 1000000100 0000110110 0111010111 1010111001 0010100111 1111001111 1000000100 0000110110 0111110111 1010101001 0010100111 1111001111 1000000100 1001101110 1100111100 0011100000 1111001010 0111100010 0000100100 1001101110 1100111100 0111100000 1111001010 0111100010 0000100100 1001101110 1100111100 0111100000 1111001010 0111100010 0000100100 1001101110 1100111100 0011100000 1111001010 0111100010 0000100100 1001101111 1100111100 0011100000 1111001010 0111100010 0000100100 1001010101 1011010011 0111100101 1001111111 0011111111 0110100110 1101010101 1011010011 0111100111 1001111111 0011111111 0111110110 1101010101 1011010011 0111100111 1001111111 0011111111 0111110110 1101010101 1011010011 0111100111 1001111111 0011111111 0111110110 1101011101 1011010011 0111110111 1001111111 0011111111 0110110110 1111101100 1111001000 0000011101 0111010110 1010000010 0110110111 1111101100 1111001000 0000011101 0111110110 1010000111 0110110101 1111101100 1111001000 0000011101 0111110110 1010000111 0110110101 1111101100 1111001000 0000011101 0111110110 1010000111 0110110101 1111101100 1111001000 0000011101 0111110110 1010000010 0110110101 1101111101 0011001110 1111110100 1001011101 0101010001 1000000110 1101111101 1011001111 1111110100 1001011101 0101110001 1000000110 1101111101 1011001111 1111110100 1001011101 0101110001 1000000110 1101111101 1011001111 1111110100 1001011111 0101110001 1000000110 1101111101 1011001111 0111100100 1001011101 1101110000 1000000110 1101111000 1100101100 0110100111 0001011000 0111111110 00111 1101111000 1100101100 0110100111 0001001110 0111111110 00111 1101111000 1100101100 0100100111 0001001110 0111111110 00111 1101111000 1100101100 0100100111 0001001110 0111111110 00111 1101101000 1100101100 0100110111 0001011010 0111110110 00111 Binary state data for primate sequences (Y/R data). This file is part of the TREE-PUZZLE distribution. ($Id$) tree-puzzle-5.2/data/primates.ctrees0000644000076400001440000001161007642375020013277 (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,(((Human,Chimpanzee),Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); (Gibbon,((Human,Chimpanzee,Gorilla),Orangutan)); tree-puzzle-5.2/data/globin.ctrees0000644000076400001440000002046407642045635012742 (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,GLB5_PETMA),LGB2_LUPLU)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),(MYG_PHYCA,(GLB5_PETMA,LGB2_LUPLU))))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,LGB2_LUPLU),GLB5_PETMA)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,LGB2_LUPLU),GLB5_PETMA)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,LGB2_LUPLU),GLB5_PETMA)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,LGB2_LUPLU),GLB5_PETMA)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,LGB2_LUPLU),GLB5_PETMA)))); (HBB_HUMAN,(HBB_HORSE,((HBA_HUMAN,HBA_HORSE),((MYG_PHYCA,LGB2_LUPLU),GLB5_PETMA)))); 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Schmidt, Korbinian Strimmer, and Arndt von Haeseler # (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, # M. Vingron, and Arndt von Haeseler # (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler # # All parts of the source except where indicated are distributed under # the GNU public licence. 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Schmidt, Korbinian Strimmer, and Arndt von Haeseler # (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, # M. Vingron, and Arndt von Haeseler # (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler # # All parts of the source except where indicated are distributed under # the GNU public licence. See http://www.opensource.org for details. # # ($Id$) # SHELL = @SHELL@ srcdir = @srcdir@ top_srcdir = @top_srcdir@ VPATH = @srcdir@ prefix = @prefix@ exec_prefix = @exec_prefix@ bindir = @bindir@ sbindir = @sbindir@ libexecdir = @libexecdir@ datadir = @datadir@ sysconfdir = @sysconfdir@ sharedstatedir = @sharedstatedir@ localstatedir = @localstatedir@ libdir = @libdir@ infodir = @infodir@ mandir = @mandir@ includedir = @includedir@ oldincludedir = /usr/include pkgdatadir = $(datadir)/@PACKAGE@ pkglibdir = $(libdir)/@PACKAGE@ pkgincludedir = $(includedir)/@PACKAGE@ top_builddir = .. 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Dasyurus .........y c..t.....g .a......a. t......... c.c......c ....c..... Echymipera t.....c..a .......... .....t.... ...c...... c.c.....ac ....c..... Trichosuru ...c.....a c.......c. .....t..ac t..a...... c.t....... ....ct.... Phalanger .........a c..t....tt ........ac a..c...... .........c .....t.... Philander t.....t..a c.t....... .a......a. t......... c.c......c .....t.... Bos t..c..t... c.c..g.... ........a. .c.a...... c.c......c ....c..... aatacattac acatcagaca catcaactgc cttctcctca gtagcacata tctgtc ......c... ..c..t.... ...tc..c.. ...t.....c .....c..c. .t.... ......c... ..t....... ..ctt..c.. t........c .....c..c. .t..c. c......... ..g....... .cct...a.. t.....a..c ..g..t..c. .t..c. ...g..c... ..cg.t..t. ..g....a.. t.....a... .....c..c. ...... ......c... ..tc.c.... .......a.. t..t..a... a.c..c..c. ...c.. t........t .......... ..ct...c.. a..t..a... .....c.... ....c. ......c... .....c.... ..a....a.. a........t ..ta.c.... ....c. Part of the mtDNA cytochrome b gene. Thomas, R. H., W. Schaffner, A. C. Wilson, and S. Pbo. 1989. DNA phylogeny of the extinct marsupial wolf. Nature 340:465-467. This file is part of the TREE-PUZZLE distribution. 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tree-puzzle-5.2/depcomp0000755000076400001440000003033507470534440010717 #! /bin/sh # depcomp - compile a program generating dependencies as side-effects # Copyright 1999, 2000 Free Software Foundation, Inc. # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2, or (at your option) # any later version. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA # 02111-1307, USA. # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that program. # Originally written by Alexandre Oliva . if test -z "$depmode" || test -z "$source" || test -z "$object"; then echo "depcomp: Variables source, object and depmode must be set" 1>&2 exit 1 fi # `libtool' can also be set to `yes' or `no'. if test -z "$depfile"; then base=`echo "$object" | sed -e 's,^.*/,,' -e 's,\.\([^.]*\)$,.P\1,'` dir=`echo "$object" | sed 's,/.*$,/,'` if test "$dir" = "$object"; then dir= fi # FIXME: should be _deps on DOS. depfile="$dir.deps/$base" fi tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`} rm -f "$tmpdepfile" # Some modes work just like other modes, but use different flags. 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AC_DEFUN([_AM_STAMP], [m4_define([_AM_STAMP_Count], m4_incr(_AM_STAMP_Count))dnl AS_ESCAPE(_AM_DIRNAME(patsubst([$1], [:.*])))/stamp-h[]_AM_STAMP_Count]) # _AM_CONFIG_HEADER(HEADER[:SOURCES], COMMANDS, INIT-COMMANDS) # ------------------------------------------------------------ # We used to try to get a real timestamp in stamp-h. But the fear is that # that will cause unnecessary cvs conflicts. AC_DEFUN([_AM_CONFIG_HEADER], [# Add the stamp file to the list of files AC keeps track of, # along with our hook. AC_CONFIG_HEADERS([$1], [# update the timestamp echo 'timestamp for $1' >"_AM_STAMP([$1])" $2], [$3]) ])# _AM_CONFIG_HEADER # AM_CONFIG_HEADER(HEADER[:SOURCES]..., COMMANDS, INIT-COMMANDS) # -------------------------------------------------------------- AC_DEFUN([AM_CONFIG_HEADER], [AC_FOREACH([_AM_File], [$1], [_AM_CONFIG_HEADER(_AM_File, [$2], [$3])]) ])# AM_CONFIG_HEADER tree-puzzle-5.2/tests/0000777000076400001440000000000010075312141010547 5tree-puzzle-5.2/tests/check-qp-jtt-rhet-clock-prot0000644000076400001440000002674210073365741015742 TREE-PUZZLE Input file name: qp-jtt-rhet-clock-prot.prot Type of analysis: tree reconstruction Parameter estimation: approximate (faster) Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) Standard errors (S.E.) are obtained by the curvature method. The upper and lower bounds of an approximate 95% confidence interval for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. SEQUENCE ALIGNMENT Input data: 7 sequences with 128 amino acid sites Number of constant sites: 7 (= 5.5% of all sites) Number of site patterns: 125 Number of constant site patterns: 5 (= 4.0% of all site patterns) SUBSTITUTION PROCESS Model of substitution: JTT (Jones et al. 1992) Amino acid frequencies (estimated from data set): pi(A) = 12.2% pi(R) = 2.3% pi(N) = 3.0% pi(D) = 4.9% pi(C) = 0.7% pi(Q) = 2.3% pi(E) = 5.4% pi(G) = 6.0% pi(H) = 5.8% pi(I) = 2.7% pi(L) = 12.5% pi(K) = 9.3% pi(M) = 1.3% pi(F) = 4.9% pi(P) = 2.6% pi(S) = 6.7% pi(T) = 4.5% pi(W) = 1.3% pi(Y) = 2.2% pi(V) = 9.4% AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) gaps wildcards sum % sequence HBB_HUMAN 0 0 0 0.00% HBB_HORSE 0 0 0 0.00% HBA_HUMAN 0 0 0 0.00% HBA_HORSE 0 0 0 0.00% MYG_PHYCA 0 0 0 0.00% GLB5_PETMA 0 0 0 0.00% LGB2_LUPLU 0 0 0 0.00% ------------------------------------------------------- Sum 0 0 0 0.00% The table above shows the amount of gaps ('-') and other 'wildcard' characters ('X', '?', etc.) and their percentage of the 128 columns in the alignment. Sequences with more than 50% ambiguous characters are marked with a '!' and should be checked, whether they have sufficient overlap to other sequences. Sequences with 100% ambiguous characters do not hold any phylogenetic information and had to be discarded from the analysis. SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) 5% chi-square test p-value HBB_HUMAN passed 92.31% HBB_HORSE passed 79.58% HBA_HUMAN passed 93.09% HBA_HORSE passed 81.20% MYG_PHYCA passed 33.23% GLB5_PETMA passed 19.11% LGB2_LUPLU passed 41.67% The chi-square tests compares the amino acid composition of each sequence to the frequency distribution assumed in the maximum likelihood model. WARNING: Result of chi-square test may not be valid because of small maximum likelihood frequencies and short sequence length! IDENTICAL SEQUENCES The sequences in each of the following groups are all identical. To speed up computation please remove all but one of each group from the data set. All sequences are unique. MAXIMUM LIKELIHOOD DISTANCES Maximum likelihood distances are computed using the selected model of substitution and rate heterogeneity. 7 HBB_HUMAN 0.00000 0.17887 1.04805 1.08480 2.52050 2.10945 3.26098 HBB_HORSE 0.17887 0.00000 1.09690 1.10752 2.49215 2.12870 3.34229 HBA_HUMAN 1.04805 1.09690 0.00000 0.12538 2.35997 1.45565 3.24727 HBA_HORSE 1.08480 1.10752 0.12538 0.00000 2.43814 1.57611 3.14845 MYG_PHYCA 2.52050 2.49215 2.35997 2.43814 0.00000 2.54103 3.42222 GLB5_PETMA 2.10945 2.12870 1.45565 1.57611 2.54103 0.00000 2.84131 LGB2_LUPLU 3.26098 3.34229 3.24727 3.14845 3.42222 2.84131 0.00000 Average distance (over all possible pairs of sequences): 2.07265 minimum : 0.12538, maximum : 3.42222 variance : 1.03523, std.dev. : 1.01746 RATE HETEROGENEITY Model of rate heterogeneity: Gamma distributed rates Gamma distribution parameter alpha (estimated from data set): 2.85 (S.E. 1.58) Number of Gamma rate categories: 8 Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability 1 0.2882 0.1250 2 0.4879 0.1250 3 0.6513 0.1250 4 0.8135 0.1250 5 0.9910 0.1250 6 1.2042 0.1250 7 1.4978 0.1250 8 2.0662 0.1250 Categories 1-8 approximate a continous Gamma-distribution with expectation 1 and variance 0.35. Combination of categories that contributes the most to the likelihood (computation done without clock assumption assuming quartet-puzzling tree): 8 1 1 8 3 2 6 4 8 1 8 2 4 1 8 4 1 8 8 8 6 6 1 8 3 3 1 4 1 6 2 8 5 8 1 8 1 4 4 7 1 8 8 1 4 2 1 6 6 1 4 4 2 2 8 1 2 7 3 1 8 8 2 5 8 8 2 4 8 4 8 3 7 6 8 8 7 1 4 8 1 1 7 8 1 2 8 1 7 6 1 1 8 1 1 6 4 2 5 7 4 1 6 8 1 2 4 8 7 4 1 5 8 6 2 8 6 6 8 3 6 6 7 2 6 4 3 1 QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) name | resolved | partly resolved | unresolved | sum -------------------------------------------------------------------------- HBB_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 HBB_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 HBA_HUMAN 19 [ 95.00%] 1 [ 5.00%] 0 [ 0.00%] 20 HBA_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 MYG_PHYCA 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 GLB5_PETMA 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 LGB2_LUPLU 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 -------------------------------------------------------------------------- #quartets : 31 [ 88.57%] 1 [ 2.86%] 3 [ 8.57%] 35 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage relative to the number of times the sequence occurs in the list of quartets (i.e. 20 quartets out of 35 in total). In fully resolved quartet one single topology is supported, while for partially resolved quartets two and for completely unresolved quartets none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. Note: Because 4 sequences are involved in one quartet numbers add up to a four-fold of the existing quartets. Hint: The overall numbers in the last row give information about the phylogenetic content of the dataset. The higher the percentage of partially and unresolved quartets, the lower the content of phylogenetic information. This can be visualized in more detail by likelihood mapping analysis. TREE SEARCH Quartet puzzling is used to choose from the possible tree topologies and to simultaneously infer support values for internal branches. Number of puzzling steps: 1000 Analysed quartets: 35 Fully resolved quartets: 31 (= 88.6%) Partly resolved quartets: 1 (= 2.9%) Unresolved quartets: 3 (= 8.6%) Quartet trees are based on approximate maximum likelihood values using the selected model of substitution and rate heterogeneity. QUARTET PUZZLING TREE Support for the internal branches of the unrooted quartet puzzling tree topology is shown in percent. This quartet puzzling tree is not completely resolved! :---MYG_PHYCA : :100:---GLB5_PETMA : : :100: :---LGB2_LUPLU : : : : :---HBA_HUMAN : :100: : :---HBA_HORSE : :-----------HBB_HORSE : :-----------HBB_HUMAN Quartet puzzling tree (in CLUSTAL W notation): (HBB_HUMAN,((MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)100,(HBA_HUMAN, HBA_HORSE)100)100,HBB_HORSE); BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) ****... : 1000 **..... : 1000 **..*** : 1000 Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen) *****.. : 393 Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen) ****.*. : 380 ****..* : 227 MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :--------------5 MYG_PHYCA :-----8 : :-------6 GLB5_PETMA : : : :-------------------7 LGB2_LUPLU :------10 : : :-3 HBA_HUMAN : :---9 : :-4 HBA_HORSE : :--2 HBB_HORSE : :-1 HBB_HUMAN branch length S.E. branch length S.E. HBB_HUMAN 1 0.04933 0.03409 8 0.50700 0.17281 HBB_HORSE 2 0.12953 0.04093 9 0.23403 0.10586 HBA_HUMAN 3 0.01995 0.02303 10 0.74732 0.14235 HBA_HORSE 4 0.10548 0.03367 MYG_PHYCA 5 1.68057 0.30228 GLB5_PETMA 6 0.81182 0.18641 12 iterations until convergence LGB2_LUPLU 7 2.33484 0.42478 log L: -1701.69 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): (HBB_HUMAN:0.04933,((MYG_PHYCA:1.68057,GLB5_PETMA:0.81182,LGB2_LUPLU:2.33484) 100:0.50700,(HBA_HUMAN:0.01995,HBA_HORSE:0.10548)100:0.23403)100:0.74732, HBB_HORSE:0.12953); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF CONSENSUS TREE (WITH CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. Root located at branch: 7 "LGB2_LUPLU" (automatic search) If the automatic search misplaces the root please rerun the analysis (rename "outtree" to "intree") and select location of root manually! :----------5 MYG_PHYCA :------8 : :----------6 GLB5_PETMA : : : :------------------7 LGB2_LUPLU :----10 : : :-3 HBA_HUMAN : :------9 : :-4 HBA_HORSE : :-2 HBB_HORSE : :-1 HBB_HUMAN Tree drawn as unrooted tree for better comparison with non-clock tree! branch length nc/c branch length nc/c (= non-clock/clock) HBB_HUMAN 1 0.08775 0.562 8 0.58020 0.874 HBB_HORSE 2 0.08775 1.476 9 0.51495 0.454 HBA_HUMAN 3 0.06493 0.307 10 0.49213 1.519 HBA_HORSE 4 0.06493 1.625 MYG_PHYCA 5 1.16008 1.449 GLB5_PETMA 6 1.16008 0.700 7 iterations until convergence LGB2_LUPLU 7 2.28806 1.020 log L: -1708.27 height S.E. of node common to branches 0.06493 0.01761 9 3 4 0.08775 0.02041 10 2 1 0.57988 0.07414 8 9 10 1.16008 0.11361 7 8 5 6 1.72407 0.21630 of root at branch 7 Rooted consensus tree with clocklike maximum likelihood branch lengths (in CLUSTAL W notation): (LGB2_LUPLU:1.72407,(((HBA_HUMAN:0.06493,HBA_HORSE:0.06493)100:0.51495 ,(HBB_HORSE:0.08775,HBB_HUMAN:0.08775):0.49213):0.58020,MYG_PHYCA:1.16008, GLB5_PETMA:1.16008):0.56399); MOLECULAR CLOCK LIKELIHOOD RATIO TEST log L without clock: -1701.69 (independent branch parameters: 10) log L with clock: -1708.27 (independent branch parameters: 5) Likelihood ratio test statistic delta: 13.15 Degress of freedom of chi-square distribution: 5 Critical significance level: 2.20% The simpler (clocklike) tree is rejected on a significance level of 5%. The log-likelihood of the more complex (no clock) tree is significantly increased. Please take care that the correct root is used! TIME STAMP tree-puzzle-5.2/tests/template-test0000755000076400001440000001622410073365600013214 #! /bin/sh # # template-test # # # Part of TREE-PUZZLE 5.2 (July 2004) # # (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler # (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, # M. Vingron, and Arndt von Haeseler # (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler # # All parts of the source except where indicated are distributed under # the GNU public licence. See http://www.opensource.org for details. # # ($Id$) # fname=`echo $0 | sed 's/.*\///'` GENERATE=0 TESTTYPE="Testing: " if test 0 -ne $# then case "$1" in -g*) GENERATE=1 TESTTYPE="Generating: " ;; *) echo "Usage: $fname [-g] " echo echo " Test a TREE-PUZZLE scenario." echo " With -g no test is performed, but the " echo " template for a future test is created." echo exit 1 ;; esac fi ########################################################################## TEST_PREF=`echo $fname | sed s/\.test//` INUTREE=${TEST_PREF}.trees INCTREE=${TEST_PREF}.ctrees PARAMS=${TEST_PREF}.param # default DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees # # data type # case "$TEST_PREF" in *-nucl) TESTTYPE="${TESTTYPE}nucleotide data" DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees echo d > $PARAMS case "$TEST_PREF" in *-hky*) TESTTYPE="${TESTTYPE}, HKY" ;; *-tn*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS ;; *-gtr*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS echo m >> $PARAMS ;; *-sh*) TESTTYPE="${TESTTYPE}, SH" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-prot) TESTTYPE="${TESTTYPE}protein data" DATA=prot INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/globin.a INUTREESOURCE=../data/globin.trees INCTREESOURCE=../data/globin.ctrees echo d > $PARAMS echo d >> $PARAMS case "$TEST_PREF" in *-dayhoff*) TESTTYPE="${TESTTYPE}, Dayhoff" echo m >> $PARAMS ;; *-jtt*) TESTTYPE="${TESTTYPE}, JTT" echo m >> $PARAMS echo m >> $PARAMS ;; *-mtrev*) TESTTYPE="${TESTTYPE}, mtREV" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-blosum*) TESTTYPE="${TESTTYPE}, BLOSUM" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-vt*) TESTTYPE="${TESTTYPE}, VT" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-wag*) TESTTYPE="${TESTTYPE}, WAG" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-bin) TESTTYPE="${TESTTYPE}binary data" DATA=bin INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/primates.b INUTREESOURCE=../data/primates.trees INCTREESOURCE=../data/primates.ctrees echo d > $PARAMS echo d >> $PARAMS echo d >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}default data, default model" ;; esac case "$TEST_PREF" in *-clock*) TESTTYPE="${TESTTYPE}, clock" echo z >> $PARAMS ;; esac case "$TEST_PREF" in *-rhet4*) TESTTYPE="${TESTTYPE}, rate heterogeneity (4 rates)" echo w >> $PARAMS echo c >> $PARAMS echo 4 >> $PARAMS ;; *-rhet*) TESTTYPE="${TESTTYPE}, rate heterogeneity" echo w >> $PARAMS ;; esac CHECK_PREF=check-$INFILE case "$TEST_PREF" in qp-*) TESTTYPE="${TESTTYPE}, quartet puzzling" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; lm-*) TESTTYPE="${TESTTYPE}, likelihood mapping" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo b >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; ut-*) TESTTYPE="${TESTTYPE}, user tree evaluation" cp $INFILESOURCE $INFILE cp $INUTREESOURCE $INUTREE RESULT_PREF=$INUTREE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INUTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; cons-*) TESTTYPE="${TESTTYPE}, consensus construction" cp $INFILESOURCE $INFILE cp $INCTREESOURCE $INCTREE RESULT_PREF=$INCTREE echo k >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INCTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; *) echo; echo "$TESTTYPE ($TEST_PREF)" echo UNKNOWN analysis type: test ignored exit 77 ;; esac if test $GENERATE == 1; then cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > check-${TEST_PREF} exit 0 else cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? exit $result fi tree-puzzle-5.2/tests/check-qp-tn-nucl0000644000076400001440000002253710073365717013507 TREE-PUZZLE Input file name: qp-tn-nucl.nucl Type of analysis: tree reconstruction Parameter estimation: approximate (faster) Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) Standard errors (S.E.) are obtained by the curvature method. The upper and lower bounds of an approximate 95% confidence interval for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. SEQUENCE ALIGNMENT Input data: 8 sequences with 116 nucleotide sites Number of constant sites: 66 (= 56.9% of all sites) Number of site patterns: 54 Number of constant site patterns: 4 (= 7.4% of all site patterns) SUBSTITUTION PROCESS Model of substitution: TN (Tamura-Nei 1993) Transition/transversion parameter (estimated from data set): 1.24 (S.E. 0.61) Y/R transition parameter (estimated from data set): 2.27 (S.E. 0.65) Rate matrix R (parameters restricted to selected model): A-C rate: 1.00000 A-G rate: 1.52641 A-T rate: 1.00000 C-G rate: 1.00000 C-T rate: 3.42338 G-T rate: 1.00000 Nucleotide frequencies (estimated from data set): pi(A) = 26.6% pi(C) = 30.6% pi(G) = 12.0% pi(T) = 30.7% Expected transition/transversion ratio: 1.57 Expected pyrimidine transition/purine transition ratio: 6.69 AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) gaps wildcards sum % sequence Thylacinus 0 0 0 0.00% Sarcophilu 0 0 0 0.00% Dasyurus 0 1 1 0.86% Echymipera 0 0 0 0.00% Trichosuru 0 0 0 0.00% Phalanger 0 0 0 0.00% Philander 0 0 0 0.00% Bos 0 0 0 0.00% ------------------------------------------------------- Sum 0 1 1 0.11% The table above shows the amount of gaps ('-') and other 'wildcard' characters ('X', '?', etc.) and their percentage of the 116 columns in the alignment. Sequences with more than 50% ambiguous characters are marked with a '!' and should be checked, whether they have sufficient overlap to other sequences. Sequences with 100% ambiguous characters do not hold any phylogenetic information and had to be discarded from the analysis. SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) 5% chi-square test p-value Thylacinus passed 90.89% Sarcophilu passed 93.32% Dasyurus passed 98.01% Echymipera passed 92.83% Trichosuru passed 90.41% Phalanger passed 86.09% Philander passed 66.19% Bos passed 60.02% The chi-square tests compares the nucleotide composition of each sequence to the frequency distribution assumed in the maximum likelihood model. IDENTICAL SEQUENCES The sequences in each of the following groups are all identical. To speed up computation please remove all but one of each group from the data set. All sequences are unique. MAXIMUM LIKELIHOOD DISTANCES Maximum likelihood distances are computed using the selected model of substitution and rate heterogeneity. 8 Thylacinus 0.00000 0.25968 0.22378 0.25026 0.26619 0.25302 0.22610 0.24162 Sarcophilu 0.25968 0.00000 0.13240 0.27376 0.28965 0.33121 0.26282 0.30169 Dasyurus 0.22378 0.13240 0.00000 0.20328 0.25274 0.25432 0.17972 0.24235 Echymipera 0.25026 0.27376 0.20328 0.00000 0.30289 0.34430 0.23479 0.27773 Trichosuru 0.26619 0.28965 0.25274 0.30289 0.00000 0.21414 0.29157 0.27782 Phalanger 0.25302 0.33121 0.25432 0.34430 0.21414 0.00000 0.29425 0.33582 Philander 0.22610 0.26282 0.17972 0.23479 0.29157 0.29425 0.00000 0.22749 Bos 0.24162 0.30169 0.24235 0.27773 0.27782 0.33582 0.22749 0.00000 Average distance (over all possible pairs of sequences): 0.25876 minimum : 0.13240, maximum : 0.34430 variance : 0.00217, std.dev. : 0.04653 RATE HETEROGENEITY Model of rate heterogeneity: uniform rate QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) name | resolved | partly resolved | unresolved | sum -------------------------------------------------------------------------- Thylacinus 21 [ 60.00%] 4 [ 11.43%] 10 [ 28.57%] 35 Sarcophilu 26 [ 74.29%] 1 [ 2.86%] 8 [ 22.86%] 35 Dasyurus 27 [ 77.14%] 2 [ 5.71%] 6 [ 17.14%] 35 Echymipera 19 [ 54.29%] 3 [ 8.57%] 13 [ 37.14%] 35 Trichosuru 25 [ 71.43%] 4 [ 11.43%] 6 [ 17.14%] 35 Phalanger 28 [ 80.00%] 1 [ 2.86%] 6 [ 17.14%] 35 Philander 23 [ 65.71%] 5 [ 14.29%] 7 [ 20.00%] 35 Bos 19 [ 54.29%] 4 [ 11.43%] 12 [ 34.29%] 35 -------------------------------------------------------------------------- #quartets : 47 [ 67.14%] 6 [ 8.57%] 17 [ 24.29%] 70 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage relative to the number of times the sequence occurs in the list of quartets (i.e. 35 quartets out of 70 in total). In fully resolved quartet one single topology is supported, while for partially resolved quartets two and for completely unresolved quartets none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. Note: Because 4 sequences are involved in one quartet numbers add up to a four-fold of the existing quartets. Hint: The overall numbers in the last row give information about the phylogenetic content of the dataset. The higher the percentage of partially and unresolved quartets, the lower the content of phylogenetic information. This can be visualized in more detail by likelihood mapping analysis. TREE SEARCH Quartet puzzling is used to choose from the possible tree topologies and to simultaneously infer support values for internal branches. Number of puzzling steps: 1000 Analysed quartets: 70 Fully resolved quartets: 47 (= 67.1%) Partly resolved quartets: 6 (= 8.6%) Unresolved quartets: 17 (= 24.3%) Quartet trees are based on approximate maximum likelihood values using the selected model of substitution and rate heterogeneity. QUARTET PUZZLING TREE Support for the internal branches of the unrooted quartet puzzling tree topology is shown in percent. This quartet puzzling tree is not completely resolved! :---Trichosuru :-----94: : :---Phalanger : : :---Sarcophilu : :-98: : : :---Dasyurus : : :-63: :---Philander : :-67: : : :---Bos : : : :-------Echymipera : :-----------Thylacinus Quartet puzzling tree (in CLUSTAL W notation): (Thylacinus,(Trichosuru,Phalanger)94,((Sarcophilu,Dasyurus)98, (Philander,Bos)67,Echymipera)63); BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) *..***** : 979 ****..** : 935 ******.. : 666 *...**.. : 629 Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen) *...**** : 422 Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen) ***.**.. : 271 *..***.. : 132 *...**.* : 122 ***.**.* : 112 *..*..** : 94 *.....** : 88 ****.... : 83 ****..*. : 79 *..*.... : 65 *....*.. : 56 *..***.* : 49 ***.***. : 40 ***..... : 36 **..**** : 21 *..*..*. : 21 *.....*. : 20 *......* : 19 *...***. : 17 ***...** : 13 ****.**. : 7 (9 other less frequent bipartitions not shown) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :---------5 Trichosuru :------9 : :----------6 Phalanger : : :----------2 Sarcophilu : :-------10 : : :-3 Dasyurus :-----12 : : :-------7 Philander : :----11 : : :-----------8 Bos : : : :------------4 Echymipera : :---------1 Thylacinus branch length S.E. branch length S.E. Thylacinus 1 0.11472 0.03957 9 0.05924 0.03453 Sarcophilu 2 0.12889 0.03726 10 0.08141 0.03441 Dasyurus 3 0.00946 0.01286 11 0.04411 0.02610 Echymipera 4 0.14312 0.04216 12 0.05429 0.03071 Trichosuru 5 0.10849 0.03850 Phalanger 6 0.12332 0.04128 Philander 7 0.09008 0.03478 7 iterations until convergence Bos 8 0.13724 0.04194 log L: -600.80 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Thylacinus:0.11472,(Trichosuru:0.10849,Phalanger:0.12332)94:0.05924, ((Sarcophilu:0.12889,Dasyurus:0.00946)98:0.08141,(Philander:0.09008, Bos:0.13724)67:0.04411,Echymipera:0.14312)63:0.05429); TIME STAMP tree-puzzle-5.2/tests/check-qp-pure-nucl0000644000076400001440000002244510073365717014037 TREE-PUZZLE Input file name: qp-pure-nucl.nucl Type of analysis: tree reconstruction Parameter estimation: approximate (faster) Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) Standard errors (S.E.) are obtained by the curvature method. The upper and lower bounds of an approximate 95% confidence interval for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. SEQUENCE ALIGNMENT Input data: 8 sequences with 116 nucleotide sites Number of constant sites: 66 (= 56.9% of all sites) Number of site patterns: 54 Number of constant site patterns: 4 (= 7.4% of all site patterns) SUBSTITUTION PROCESS Model of substitution: HKY (Hasegawa et al. 1985) Transition/transversion parameter (estimated from data set): 1.51 (S.E. 0.28) Rate matrix R (parameters restricted to selected model): A-C rate: 1.00000 A-G rate: 2.98614 A-T rate: 1.00000 C-G rate: 1.00000 C-T rate: 2.98614 G-T rate: 1.00000 Nucleotide frequencies (estimated from data set): pi(A) = 26.6% pi(C) = 30.6% pi(G) = 12.0% pi(T) = 30.7% Expected transition/transversion ratio: 1.60 Expected pyrimidine transition/purine transition ratio: 2.95 AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) gaps wildcards sum % sequence Thylacinus 0 0 0 0.00% Sarcophilu 0 0 0 0.00% Dasyurus 0 1 1 0.86% Echymipera 0 0 0 0.00% Trichosuru 0 0 0 0.00% Phalanger 0 0 0 0.00% Philander 0 0 0 0.00% Bos 0 0 0 0.00% ------------------------------------------------------- Sum 0 1 1 0.11% The table above shows the amount of gaps ('-') and other 'wildcard' characters ('X', '?', etc.) and their percentage of the 116 columns in the alignment. Sequences with more than 50% ambiguous characters are marked with a '!' and should be checked, whether they have sufficient overlap to other sequences. Sequences with 100% ambiguous characters do not hold any phylogenetic information and had to be discarded from the analysis. SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) 5% chi-square test p-value Thylacinus passed 90.89% Sarcophilu passed 93.32% Dasyurus passed 98.01% Echymipera passed 92.83% Trichosuru passed 90.41% Phalanger passed 86.09% Philander passed 66.19% Bos passed 60.02% The chi-square tests compares the nucleotide composition of each sequence to the frequency distribution assumed in the maximum likelihood model. IDENTICAL SEQUENCES The sequences in each of the following groups are all identical. To speed up computation please remove all but one of each group from the data set. All sequences are unique. MAXIMUM LIKELIHOOD DISTANCES Maximum likelihood distances are computed using the selected model of substitution and rate heterogeneity. 8 Thylacinus 0.00000 0.25562 0.22032 0.24509 0.26007 0.24938 0.22246 0.23734 Sarcophilu 0.25562 0.00000 0.13169 0.26969 0.28414 0.32680 0.26008 0.29786 Dasyurus 0.22032 0.13169 0.00000 0.20032 0.24821 0.25234 0.17801 0.23883 Echymipera 0.24509 0.26969 0.20032 0.00000 0.29531 0.33871 0.23041 0.27215 Trichosuru 0.26007 0.28414 0.24821 0.29531 0.00000 0.21136 0.28562 0.27148 Phalanger 0.24938 0.32680 0.25234 0.33871 0.21136 0.00000 0.29036 0.33042 Philander 0.22246 0.26008 0.17801 0.23041 0.28562 0.29036 0.00000 0.22452 Bos 0.23734 0.29786 0.23883 0.27215 0.27148 0.33042 0.22452 0.00000 Average distance (over all possible pairs of sequences): 0.25459 minimum : 0.13169, maximum : 0.33871 variance : 0.00207, std.dev. : 0.04544 RATE HETEROGENEITY Model of rate heterogeneity: uniform rate QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) name | resolved | partly resolved | unresolved | sum -------------------------------------------------------------------------- Thylacinus 22 [ 62.86%] 4 [ 11.43%] 9 [ 25.71%] 35 Sarcophilu 27 [ 77.14%] 1 [ 2.86%] 7 [ 20.00%] 35 Dasyurus 27 [ 77.14%] 4 [ 11.43%] 4 [ 11.43%] 35 Echymipera 20 [ 57.14%] 4 [ 11.43%] 11 [ 31.43%] 35 Trichosuru 27 [ 77.14%] 2 [ 5.71%] 6 [ 17.14%] 35 Phalanger 28 [ 80.00%] 3 [ 8.57%] 4 [ 11.43%] 35 Philander 25 [ 71.43%] 6 [ 17.14%] 4 [ 11.43%] 35 Bos 20 [ 57.14%] 4 [ 11.43%] 11 [ 31.43%] 35 -------------------------------------------------------------------------- #quartets : 49 [ 70.00%] 7 [ 10.00%] 14 [ 20.00%] 70 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage relative to the number of times the sequence occurs in the list of quartets (i.e. 35 quartets out of 70 in total). In fully resolved quartet one single topology is supported, while for partially resolved quartets two and for completely unresolved quartets none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. Note: Because 4 sequences are involved in one quartet numbers add up to a four-fold of the existing quartets. Hint: The overall numbers in the last row give information about the phylogenetic content of the dataset. The higher the percentage of partially and unresolved quartets, the lower the content of phylogenetic information. This can be visualized in more detail by likelihood mapping analysis. TREE SEARCH Quartet puzzling is used to choose from the possible tree topologies and to simultaneously infer support values for internal branches. Number of puzzling steps: 1000 Analysed quartets: 70 Fully resolved quartets: 49 (= 70.0%) Partly resolved quartets: 7 (= 10.0%) Unresolved quartets: 14 (= 20.0%) Quartet trees are based on approximate maximum likelihood values using the selected model of substitution and rate heterogeneity. QUARTET PUZZLING TREE Support for the internal branches of the unrooted quartet puzzling tree topology is shown in percent. This quartet puzzling tree is not completely resolved! :---Trichosuru :-----97: : :---Phalanger : : :---Sarcophilu : :-98: : : :---Dasyurus : : :-71: :---Philander : :-65: : : :---Bos : : : :-------Echymipera : :-----------Thylacinus Quartet puzzling tree (in CLUSTAL W notation): (Thylacinus,(Trichosuru,Phalanger)97,((Sarcophilu,Dasyurus)98, (Philander,Bos)65,Echymipera)71); BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) *..***** : 981 ****..** : 971 *...**.. : 713 ******.. : 649 Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen) *...**** : 426 Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen) ***.**.. : 347 ***.**.* : 150 *...**.* : 131 *..***.. : 87 *..*..** : 81 *.....** : 72 ****..*. : 55 ***.***. : 37 ****.... : 36 *..***.* : 36 ***..... : 31 *.....*. : 28 *...***. : 27 *......* : 27 *....*.. : 26 *..*.... : 21 **..**** : 16 ***...** : 14 *..*..*. : 13 *..****. : 12 (6 other less frequent bipartitions not shown) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :---------5 Trichosuru :------9 : :----------6 Phalanger : : :-----------2 Sarcophilu : :-------10 : : :-3 Dasyurus :-----12 : : :--------7 Philander : :----11 : : :-----------8 Bos : : : :------------4 Echymipera : :---------1 Thylacinus branch length S.E. branch length S.E. Thylacinus 1 0.11024 0.03812 9 0.05953 0.03382 Sarcophilu 2 0.13180 0.03734 10 0.08585 0.03452 Dasyurus 3 0.00572 0.01273 11 0.04220 0.02513 Echymipera 4 0.13997 0.04108 12 0.05457 0.02998 Trichosuru 5 0.10654 0.03770 Phalanger 6 0.12258 0.04064 Philander 7 0.08995 0.03428 8 iterations until convergence Bos 8 0.13479 0.04095 log L: -603.37 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Thylacinus:0.11024,(Trichosuru:0.10654,Phalanger:0.12258)97:0.05953, ((Sarcophilu:0.13180,Dasyurus:0.00572)98:0.08585,(Philander:0.08995, Bos:0.13479)65:0.04220,Echymipera:0.13997)71:0.05457); TIME STAMP tree-puzzle-5.2/tests/check-qp-pure-prot0000644000076400001440000002077310073365722014060 TREE-PUZZLE Input file name: qp-pure-prot.prot Type of analysis: tree reconstruction Parameter estimation: approximate (faster) Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) Standard errors (S.E.) are obtained by the curvature method. The upper and lower bounds of an approximate 95% confidence interval for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. SEQUENCE ALIGNMENT Input data: 7 sequences with 128 amino acid sites Number of constant sites: 7 (= 5.5% of all sites) Number of site patterns: 125 Number of constant site patterns: 5 (= 4.0% of all site patterns) SUBSTITUTION PROCESS Model of substitution: Dayhoff (Dayhoff et al. 1978) Amino acid frequencies (estimated from data set): pi(A) = 12.2% pi(R) = 2.3% pi(N) = 3.0% pi(D) = 4.9% pi(C) = 0.7% pi(Q) = 2.3% pi(E) = 5.4% pi(G) = 6.0% pi(H) = 5.8% pi(I) = 2.7% pi(L) = 12.5% pi(K) = 9.3% pi(M) = 1.3% pi(F) = 4.9% pi(P) = 2.6% pi(S) = 6.7% pi(T) = 4.5% pi(W) = 1.3% pi(Y) = 2.2% pi(V) = 9.4% AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) gaps wildcards sum % sequence HBB_HUMAN 0 0 0 0.00% HBB_HORSE 0 0 0 0.00% HBA_HUMAN 0 0 0 0.00% HBA_HORSE 0 0 0 0.00% MYG_PHYCA 0 0 0 0.00% GLB5_PETMA 0 0 0 0.00% LGB2_LUPLU 0 0 0 0.00% ------------------------------------------------------- Sum 0 0 0 0.00% The table above shows the amount of gaps ('-') and other 'wildcard' characters ('X', '?', etc.) and their percentage of the 128 columns in the alignment. Sequences with more than 50% ambiguous characters are marked with a '!' and should be checked, whether they have sufficient overlap to other sequences. Sequences with 100% ambiguous characters do not hold any phylogenetic information and had to be discarded from the analysis. SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) 5% chi-square test p-value HBB_HUMAN passed 92.31% HBB_HORSE passed 79.58% HBA_HUMAN passed 93.09% HBA_HORSE passed 81.20% MYG_PHYCA passed 33.23% GLB5_PETMA passed 19.11% LGB2_LUPLU passed 41.67% The chi-square tests compares the amino acid composition of each sequence to the frequency distribution assumed in the maximum likelihood model. WARNING: Result of chi-square test may not be valid because of small maximum likelihood frequencies and short sequence length! IDENTICAL SEQUENCES The sequences in each of the following groups are all identical. To speed up computation please remove all but one of each group from the data set. All sequences are unique. MAXIMUM LIKELIHOOD DISTANCES Maximum likelihood distances are computed using the selected model of substitution and rate heterogeneity. 7 HBB_HUMAN 0.00000 0.17425 0.96068 0.99267 2.12932 1.77231 2.78644 HBB_HORSE 0.17425 0.00000 1.01062 1.02118 2.09456 1.78465 2.86187 HBA_HUMAN 0.96068 1.01062 0.00000 0.12147 1.93540 1.30123 2.54730 HBA_HORSE 0.99267 1.02118 0.12147 0.00000 2.00515 1.39193 2.51172 MYG_PHYCA 2.12932 2.09456 1.93540 2.00515 0.00000 2.12347 2.79386 GLB5_PETMA 1.77231 1.78465 1.30123 1.39193 2.12347 0.00000 2.18272 LGB2_LUPLU 2.78644 2.86187 2.54730 2.51172 2.79386 2.18272 0.00000 Average distance (over all possible pairs of sequences): 1.73823 minimum : 0.12147, maximum : 2.86187 variance : 0.65214, std.dev. : 0.80755 RATE HETEROGENEITY Model of rate heterogeneity: uniform rate QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) name | resolved | partly resolved | unresolved | sum -------------------------------------------------------------------------- HBB_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 HBB_HORSE 20 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 20 HBA_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 HBA_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 MYG_PHYCA 17 [ 85.00%] 0 [ 0.00%] 3 [ 15.00%] 20 GLB5_PETMA 17 [ 85.00%] 0 [ 0.00%] 3 [ 15.00%] 20 LGB2_LUPLU 17 [ 85.00%] 0 [ 0.00%] 3 [ 15.00%] 20 -------------------------------------------------------------------------- #quartets : 32 [ 91.43%] 0 [ 0.00%] 3 [ 8.57%] 35 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage relative to the number of times the sequence occurs in the list of quartets (i.e. 20 quartets out of 35 in total). In fully resolved quartet one single topology is supported, while for partially resolved quartets two and for completely unresolved quartets none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. Note: Because 4 sequences are involved in one quartet numbers add up to a four-fold of the existing quartets. Hint: The overall numbers in the last row give information about the phylogenetic content of the dataset. The higher the percentage of partially and unresolved quartets, the lower the content of phylogenetic information. This can be visualized in more detail by likelihood mapping analysis. TREE SEARCH Quartet puzzling is used to choose from the possible tree topologies and to simultaneously infer support values for internal branches. Number of puzzling steps: 1000 Analysed quartets: 35 Fully resolved quartets: 32 (= 91.4%) Partly resolved quartets: 0 (= 0.0%) Unresolved quartets: 3 (= 8.6%) Quartet trees are based on approximate maximum likelihood values using the selected model of substitution and rate heterogeneity. QUARTET PUZZLING TREE Support for the internal branches of the unrooted quartet puzzling tree topology is shown in percent. This quartet puzzling tree is completely resolved. :---HBA_HUMAN :----100: : :---HBA_HORSE :100: : : :---GLB5_PETMA : : :-54: : :100: :---LGB2_LUPLU : : : :-------MYG_PHYCA : :---------------HBB_HORSE : :---------------HBB_HUMAN Quartet puzzling tree (in CLUSTAL W notation): (HBB_HUMAN,((HBA_HUMAN,HBA_HORSE)100,((GLB5_PETMA,LGB2_LUPLU)54, MYG_PHYCA)100)100,HBB_HORSE); BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) **..... : 1000 **..*** : 1000 ****... : 1000 *****.. : 544 Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen) None (No congruent split not included) Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen) ****.*. : 234 ****..* : 222 MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :-3 HBA_HUMAN :----8 : :-4 HBA_HORSE :------11 : : :------6 GLB5_PETMA : : :---9 : : : :----------------7 LGB2_LUPLU : :----10 : :-------------5 MYG_PHYCA : :--2 HBB_HORSE : :-1 HBB_HUMAN branch length S.E. branch length S.E. HBB_HUMAN 1 0.04915 0.03158 8 0.28345 0.08777 HBB_HORSE 2 0.12603 0.03871 9 0.18154 0.13086 HBA_HUMAN 3 0.02555 0.02185 10 0.34694 0.12552 HBA_HORSE 4 0.09542 0.03153 11 0.60239 0.11261 MYG_PHYCA 5 1.33166 0.21117 GLB5_PETMA 6 0.57466 0.13843 10 iterations until convergence LGB2_LUPLU 7 1.71333 0.27645 log L: -1699.00 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): (HBB_HUMAN:0.04915,((HBA_HUMAN:0.02555,HBA_HORSE:0.09542)100:0.28345, ((GLB5_PETMA:0.57466,LGB2_LUPLU:1.71333)54:0.18154,MYG_PHYCA:1.33166) 100:0.34694)100:0.60239,HBB_HORSE:0.12603); TIME STAMP tree-puzzle-5.2/tests/build-puzzle0000755000076400001440000000002307643056463013055 #! /bin/sh exit 77 tree-puzzle-5.2/tests/build-remark0000755000076400001440000000233710071267241013002 #! /bin/sh echo echo "***" echo "*** !!! Important remark !!!" echo "***" echo "*** Please note that only the output file *.puzzle is checked" echo "*** for identity. The overall precision reached in the program" echo "*** is heavily dependent on the compiler as well as the optimization" echo "*** level (-O) used to compile the executable." echo "*** Hence, even if tests are marked as failed this might just be" echo "*** due to differences in less significant digits caused by rounding" echo "*** errors from less acurate computations for the sake of faster" echo "*** running times. (If you want to be sure about this please refer" echo "*** to your compiler's manual!)" echo "***" echo "*** Please check the output file differences which are printed during the tests." echo "*** The template files which the results are checked against have been" echo "*** generated with TREE-PUZZLE 5.2 compiled with GCC version 3.3-20030226" echo "*** and default compiler flags '-g -O2' and using the SPRNG random number" echo "*** generator." echo "***" echo exit 77 tree-puzzle-5.2/tests/qp-pure-nucl.test0000755000076400001440000001622410073365716013742 #! /bin/sh # # template-test # # # Part of TREE-PUZZLE 5.2 (July 2004) # # (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler # (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, # M. Vingron, and Arndt von Haeseler # (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler # # All parts of the source except where indicated are distributed under # the GNU public licence. See http://www.opensource.org for details. # # ($Id$) # fname=`echo $0 | sed 's/.*\///'` GENERATE=0 TESTTYPE="Testing: " if test 0 -ne $# then case "$1" in -g*) GENERATE=1 TESTTYPE="Generating: " ;; *) echo "Usage: $fname [-g] " echo echo " Test a TREE-PUZZLE scenario." echo " With -g no test is performed, but the " echo " template for a future test is created." echo exit 1 ;; esac fi ########################################################################## TEST_PREF=`echo $fname | sed s/\.test//` INUTREE=${TEST_PREF}.trees INCTREE=${TEST_PREF}.ctrees PARAMS=${TEST_PREF}.param # default DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees # # data type # case "$TEST_PREF" in *-nucl) TESTTYPE="${TESTTYPE}nucleotide data" DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees echo d > $PARAMS case "$TEST_PREF" in *-hky*) TESTTYPE="${TESTTYPE}, HKY" ;; *-tn*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS ;; *-gtr*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS echo m >> $PARAMS ;; *-sh*) TESTTYPE="${TESTTYPE}, SH" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-prot) TESTTYPE="${TESTTYPE}protein data" DATA=prot INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/globin.a INUTREESOURCE=../data/globin.trees INCTREESOURCE=../data/globin.ctrees echo d > $PARAMS echo d >> $PARAMS case "$TEST_PREF" in *-dayhoff*) TESTTYPE="${TESTTYPE}, Dayhoff" echo m >> $PARAMS ;; *-jtt*) TESTTYPE="${TESTTYPE}, JTT" echo m >> $PARAMS echo m >> $PARAMS ;; *-mtrev*) TESTTYPE="${TESTTYPE}, mtREV" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-blosum*) TESTTYPE="${TESTTYPE}, BLOSUM" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-vt*) TESTTYPE="${TESTTYPE}, VT" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-wag*) TESTTYPE="${TESTTYPE}, WAG" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-bin) TESTTYPE="${TESTTYPE}binary data" DATA=bin INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/primates.b INUTREESOURCE=../data/primates.trees INCTREESOURCE=../data/primates.ctrees echo d > $PARAMS echo d >> $PARAMS echo d >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}default data, default model" ;; esac case "$TEST_PREF" in *-clock*) TESTTYPE="${TESTTYPE}, clock" echo z >> $PARAMS ;; esac case "$TEST_PREF" in *-rhet4*) TESTTYPE="${TESTTYPE}, rate heterogeneity (4 rates)" echo w >> $PARAMS echo c >> $PARAMS echo 4 >> $PARAMS ;; *-rhet*) TESTTYPE="${TESTTYPE}, rate heterogeneity" echo w >> $PARAMS ;; esac CHECK_PREF=check-$INFILE case "$TEST_PREF" in qp-*) TESTTYPE="${TESTTYPE}, quartet puzzling" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; lm-*) TESTTYPE="${TESTTYPE}, likelihood mapping" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo b >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; ut-*) TESTTYPE="${TESTTYPE}, user tree evaluation" cp $INFILESOURCE $INFILE cp $INUTREESOURCE $INUTREE RESULT_PREF=$INUTREE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INUTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; cons-*) TESTTYPE="${TESTTYPE}, consensus construction" cp $INFILESOURCE $INFILE cp $INCTREESOURCE $INCTREE RESULT_PREF=$INCTREE echo k >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INCTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; *) echo; echo "$TESTTYPE ($TEST_PREF)" echo UNKNOWN analysis type: test ignored exit 77 ;; esac if test $GENERATE == 1; then cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > check-${TEST_PREF} exit 0 else cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? exit $result fi tree-puzzle-5.2/tests/qp-mtrev-prot.test0000755000076400001440000001622410073365716014147 #! /bin/sh # # template-test # # # Part of TREE-PUZZLE 5.2 (July 2004) # # (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler # (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, # M. Vingron, and Arndt von Haeseler # (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler # # All parts of the source except where indicated are distributed under # the GNU public licence. See http://www.opensource.org for details. # # ($Id$) # fname=`echo $0 | sed 's/.*\///'` GENERATE=0 TESTTYPE="Testing: " if test 0 -ne $# then case "$1" in -g*) GENERATE=1 TESTTYPE="Generating: " ;; *) echo "Usage: $fname [-g] " echo echo " Test a TREE-PUZZLE scenario." echo " With -g no test is performed, but the " echo " template for a future test is created." echo exit 1 ;; esac fi ########################################################################## TEST_PREF=`echo $fname | sed s/\.test//` INUTREE=${TEST_PREF}.trees INCTREE=${TEST_PREF}.ctrees PARAMS=${TEST_PREF}.param # default DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees # # data type # case "$TEST_PREF" in *-nucl) TESTTYPE="${TESTTYPE}nucleotide data" DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees echo d > $PARAMS case "$TEST_PREF" in *-hky*) TESTTYPE="${TESTTYPE}, HKY" ;; *-tn*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS ;; *-gtr*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS echo m >> $PARAMS ;; *-sh*) TESTTYPE="${TESTTYPE}, SH" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-prot) TESTTYPE="${TESTTYPE}protein data" DATA=prot INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/globin.a INUTREESOURCE=../data/globin.trees INCTREESOURCE=../data/globin.ctrees echo d > $PARAMS echo d >> $PARAMS case "$TEST_PREF" in *-dayhoff*) TESTTYPE="${TESTTYPE}, Dayhoff" echo m >> $PARAMS ;; *-jtt*) TESTTYPE="${TESTTYPE}, JTT" echo m >> $PARAMS echo m >> $PARAMS ;; *-mtrev*) TESTTYPE="${TESTTYPE}, mtREV" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-blosum*) TESTTYPE="${TESTTYPE}, BLOSUM" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-vt*) TESTTYPE="${TESTTYPE}, VT" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-wag*) TESTTYPE="${TESTTYPE}, WAG" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-bin) TESTTYPE="${TESTTYPE}binary data" DATA=bin INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/primates.b INUTREESOURCE=../data/primates.trees INCTREESOURCE=../data/primates.ctrees echo d > $PARAMS echo d >> $PARAMS echo d >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}default data, default model" ;; esac case "$TEST_PREF" in *-clock*) TESTTYPE="${TESTTYPE}, clock" echo z >> $PARAMS ;; esac case "$TEST_PREF" in *-rhet4*) TESTTYPE="${TESTTYPE}, rate heterogeneity (4 rates)" echo w >> $PARAMS echo c >> $PARAMS echo 4 >> $PARAMS ;; *-rhet*) TESTTYPE="${TESTTYPE}, rate heterogeneity" echo w >> $PARAMS ;; esac CHECK_PREF=check-$INFILE case "$TEST_PREF" in qp-*) TESTTYPE="${TESTTYPE}, quartet puzzling" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; lm-*) TESTTYPE="${TESTTYPE}, likelihood mapping" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo b >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; ut-*) TESTTYPE="${TESTTYPE}, user tree evaluation" cp $INFILESOURCE $INFILE cp $INUTREESOURCE $INUTREE RESULT_PREF=$INUTREE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INUTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; cons-*) TESTTYPE="${TESTTYPE}, consensus construction" cp $INFILESOURCE $INFILE cp $INCTREESOURCE $INCTREE RESULT_PREF=$INCTREE echo k >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INCTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; *) echo; echo "$TESTTYPE ($TEST_PREF)" echo UNKNOWN analysis type: test ignored exit 77 ;; esac if test $GENERATE == 1; then cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > check-${TEST_PREF} exit 0 else cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? exit $result fi tree-puzzle-5.2/tests/check-qp-mtrev-prot0000644000076400001440000002062610073365722014237 TREE-PUZZLE Input file name: qp-mtrev-prot.prot Type of analysis: tree reconstruction Parameter estimation: approximate (faster) Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) Standard errors (S.E.) are obtained by the curvature method. The upper and lower bounds of an approximate 95% confidence interval for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. SEQUENCE ALIGNMENT Input data: 7 sequences with 128 amino acid sites Number of constant sites: 7 (= 5.5% of all sites) Number of site patterns: 125 Number of constant site patterns: 5 (= 4.0% of all site patterns) SUBSTITUTION PROCESS Model of substitution: mtREV24 (Adachi-Hasegawa 1996) Amino acid frequencies (estimated from data set): pi(A) = 12.2% pi(R) = 2.3% pi(N) = 3.0% pi(D) = 4.9% pi(C) = 0.7% pi(Q) = 2.3% pi(E) = 5.4% pi(G) = 6.0% pi(H) = 5.8% pi(I) = 2.7% pi(L) = 12.5% pi(K) = 9.3% pi(M) = 1.3% pi(F) = 4.9% pi(P) = 2.6% pi(S) = 6.7% pi(T) = 4.5% pi(W) = 1.3% pi(Y) = 2.2% pi(V) = 9.4% AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) gaps wildcards sum % sequence HBB_HUMAN 0 0 0 0.00% HBB_HORSE 0 0 0 0.00% HBA_HUMAN 0 0 0 0.00% HBA_HORSE 0 0 0 0.00% MYG_PHYCA 0 0 0 0.00% GLB5_PETMA 0 0 0 0.00% LGB2_LUPLU 0 0 0 0.00% ------------------------------------------------------- Sum 0 0 0 0.00% The table above shows the amount of gaps ('-') and other 'wildcard' characters ('X', '?', etc.) and their percentage of the 128 columns in the alignment. Sequences with more than 50% ambiguous characters are marked with a '!' and should be checked, whether they have sufficient overlap to other sequences. Sequences with 100% ambiguous characters do not hold any phylogenetic information and had to be discarded from the analysis. SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) 5% chi-square test p-value HBB_HUMAN passed 92.31% HBB_HORSE passed 79.58% HBA_HUMAN passed 93.09% HBA_HORSE passed 81.20% MYG_PHYCA passed 33.23% GLB5_PETMA passed 19.11% LGB2_LUPLU passed 41.67% The chi-square tests compares the amino acid composition of each sequence to the frequency distribution assumed in the maximum likelihood model. WARNING: Result of chi-square test may not be valid because of small maximum likelihood frequencies and short sequence length! IDENTICAL SEQUENCES The sequences in each of the following groups are all identical. To speed up computation please remove all but one of each group from the data set. All sequences are unique. MAXIMUM LIKELIHOOD DISTANCES Maximum likelihood distances are computed using the selected model of substitution and rate heterogeneity. 7 HBB_HUMAN 0.00000 0.19615 1.12348 1.16856 2.59690 2.15305 3.47989 HBB_HORSE 0.19615 0.00000 1.17857 1.20524 2.74793 2.18071 3.63316 HBA_HUMAN 1.12348 1.17857 0.00000 0.13144 2.41361 1.43785 3.06000 HBA_HORSE 1.16856 1.20524 0.13144 0.00000 2.44163 1.55582 3.05140 MYG_PHYCA 2.59690 2.74793 2.41361 2.44163 0.00000 2.62256 3.47779 GLB5_PETMA 2.15305 2.18071 1.43785 1.55582 2.62256 0.00000 2.97722 LGB2_LUPLU 3.47989 3.63316 3.06000 3.05140 3.47779 2.97722 0.00000 Average distance (over all possible pairs of sequences): 2.13490 minimum : 0.13144, maximum : 3.63316 variance : 1.07966, std.dev. : 1.03906 RATE HETEROGENEITY Model of rate heterogeneity: uniform rate QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) name | resolved | partly resolved | unresolved | sum -------------------------------------------------------------------------- HBB_HUMAN 18 [ 90.00%] 1 [ 5.00%] 1 [ 5.00%] 20 HBB_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 HBA_HUMAN 19 [ 95.00%] 1 [ 5.00%] 0 [ 0.00%] 20 HBA_HORSE 18 [ 90.00%] 2 [ 10.00%] 0 [ 0.00%] 20 MYG_PHYCA 15 [ 75.00%] 3 [ 15.00%] 2 [ 10.00%] 20 GLB5_PETMA 15 [ 75.00%] 3 [ 15.00%] 2 [ 10.00%] 20 LGB2_LUPLU 16 [ 80.00%] 2 [ 10.00%] 2 [ 10.00%] 20 -------------------------------------------------------------------------- #quartets : 30 [ 85.71%] 3 [ 8.57%] 2 [ 5.71%] 35 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage relative to the number of times the sequence occurs in the list of quartets (i.e. 20 quartets out of 35 in total). In fully resolved quartet one single topology is supported, while for partially resolved quartets two and for completely unresolved quartets none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. Note: Because 4 sequences are involved in one quartet numbers add up to a four-fold of the existing quartets. Hint: The overall numbers in the last row give information about the phylogenetic content of the dataset. The higher the percentage of partially and unresolved quartets, the lower the content of phylogenetic information. This can be visualized in more detail by likelihood mapping analysis. TREE SEARCH Quartet puzzling is used to choose from the possible tree topologies and to simultaneously infer support values for internal branches. Number of puzzling steps: 1000 Analysed quartets: 35 Fully resolved quartets: 30 (= 85.7%) Partly resolved quartets: 3 (= 8.6%) Unresolved quartets: 2 (= 5.7%) Quartet trees are based on approximate maximum likelihood values using the selected model of substitution and rate heterogeneity. QUARTET PUZZLING TREE Support for the internal branches of the unrooted quartet puzzling tree topology is shown in percent. This quartet puzzling tree is not completely resolved! :---HBA_HUMAN :100: : :---HBA_HORSE :100: : : :---MYG_PHYCA : : : : :-97:---GLB5_PETMA : : : :---LGB2_LUPLU : :-----------HBB_HORSE : :-----------HBB_HUMAN Quartet puzzling tree (in CLUSTAL W notation): (HBB_HUMAN,((HBA_HUMAN,HBA_HORSE)100,(MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)97)100, HBB_HORSE); BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) **..... : 1000 **..*** : 1000 ****... : 971 Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen) ****.*. : 462 Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen) *****.. : 436 ****..* : 100 **..*.* : 15 **..*.. : 14 **....* : 2 MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :-3 HBA_HUMAN :----8 : :-4 HBA_HORSE :------10 : : :------------5 MYG_PHYCA : :----9 : :-------6 GLB5_PETMA : : : :----------------7 LGB2_LUPLU : :--2 HBB_HORSE : :-1 HBB_HUMAN branch length S.E. branch length S.E. HBB_HUMAN 1 0.03472 0.03059 8 0.30126 0.09575 HBB_HORSE 2 0.16246 0.04359 9 0.34149 0.13763 HBA_HUMAN 3 0.04636 0.02527 10 0.70896 0.13056 HBA_HORSE 4 0.08355 0.03082 MYG_PHYCA 5 1.58550 0.26736 GLB5_PETMA 6 0.88663 0.17157 10 iterations until convergence LGB2_LUPLU 7 2.13259 0.35215 log L: -1736.55 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): (HBB_HUMAN:0.03472,((HBA_HUMAN:0.04636,HBA_HORSE:0.08355)100:0.30126, (MYG_PHYCA:1.58550,GLB5_PETMA:0.88663,LGB2_LUPLU:2.13259)97:0.34149) 100:0.70896,HBB_HORSE:0.16246); TIME STAMP tree-puzzle-5.2/tests/qp-vt-prot.test0000755000076400001440000001622410073365716013443 #! /bin/sh # # template-test # # # Part of TREE-PUZZLE 5.2 (July 2004) # # (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler # (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, # M. Vingron, and Arndt von Haeseler # (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler # # All parts of the source except where indicated are distributed under # the GNU public licence. See http://www.opensource.org for details. # # ($Id$) # fname=`echo $0 | sed 's/.*\///'` GENERATE=0 TESTTYPE="Testing: " if test 0 -ne $# then case "$1" in -g*) GENERATE=1 TESTTYPE="Generating: " ;; *) echo "Usage: $fname [-g] " echo echo " Test a TREE-PUZZLE scenario." echo " With -g no test is performed, but the " echo " template for a future test is created." echo exit 1 ;; esac fi ########################################################################## TEST_PREF=`echo $fname | sed s/\.test//` INUTREE=${TEST_PREF}.trees INCTREE=${TEST_PREF}.ctrees PARAMS=${TEST_PREF}.param # default DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees # # data type # case "$TEST_PREF" in *-nucl) TESTTYPE="${TESTTYPE}nucleotide data" DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees echo d > $PARAMS case "$TEST_PREF" in *-hky*) TESTTYPE="${TESTTYPE}, HKY" ;; *-tn*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS ;; *-gtr*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS echo m >> $PARAMS ;; *-sh*) TESTTYPE="${TESTTYPE}, SH" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-prot) TESTTYPE="${TESTTYPE}protein data" DATA=prot INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/globin.a INUTREESOURCE=../data/globin.trees INCTREESOURCE=../data/globin.ctrees echo d > $PARAMS echo d >> $PARAMS case "$TEST_PREF" in *-dayhoff*) TESTTYPE="${TESTTYPE}, Dayhoff" echo m >> $PARAMS ;; *-jtt*) TESTTYPE="${TESTTYPE}, JTT" echo m >> $PARAMS echo m >> $PARAMS ;; *-mtrev*) TESTTYPE="${TESTTYPE}, mtREV" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-blosum*) TESTTYPE="${TESTTYPE}, BLOSUM" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-vt*) TESTTYPE="${TESTTYPE}, VT" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-wag*) TESTTYPE="${TESTTYPE}, WAG" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-bin) TESTTYPE="${TESTTYPE}binary data" DATA=bin INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/primates.b INUTREESOURCE=../data/primates.trees INCTREESOURCE=../data/primates.ctrees echo d > $PARAMS echo d >> $PARAMS echo d >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}default data, default model" ;; esac case "$TEST_PREF" in *-clock*) TESTTYPE="${TESTTYPE}, clock" echo z >> $PARAMS ;; esac case "$TEST_PREF" in *-rhet4*) TESTTYPE="${TESTTYPE}, rate heterogeneity (4 rates)" echo w >> $PARAMS echo c >> $PARAMS echo 4 >> $PARAMS ;; *-rhet*) TESTTYPE="${TESTTYPE}, rate heterogeneity" echo w >> $PARAMS ;; esac CHECK_PREF=check-$INFILE case "$TEST_PREF" in qp-*) TESTTYPE="${TESTTYPE}, quartet puzzling" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; lm-*) TESTTYPE="${TESTTYPE}, likelihood mapping" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo b >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; ut-*) TESTTYPE="${TESTTYPE}, user tree evaluation" cp $INFILESOURCE $INFILE cp $INUTREESOURCE $INUTREE RESULT_PREF=$INUTREE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INUTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; cons-*) TESTTYPE="${TESTTYPE}, consensus construction" cp $INFILESOURCE $INFILE cp $INCTREESOURCE $INCTREE RESULT_PREF=$INCTREE echo k >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INCTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; *) echo; echo "$TESTTYPE ($TEST_PREF)" echo UNKNOWN analysis type: test ignored exit 77 ;; esac if test $GENERATE == 1; then cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > check-${TEST_PREF} exit 0 else cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? exit $result fi tree-puzzle-5.2/tests/qp-hky-clock-nucl.test0000755000076400001440000001622410073365716014653 #! /bin/sh # # template-test # # # Part of TREE-PUZZLE 5.2 (July 2004) # # (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler # (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, # M. Vingron, and Arndt von Haeseler # (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler # # All parts of the source except where indicated are distributed under # the GNU public licence. See http://www.opensource.org for details. # # ($Id$) # fname=`echo $0 | sed 's/.*\///'` GENERATE=0 TESTTYPE="Testing: " if test 0 -ne $# then case "$1" in -g*) GENERATE=1 TESTTYPE="Generating: " ;; *) echo "Usage: $fname [-g] " echo echo " Test a TREE-PUZZLE scenario." echo " With -g no test is performed, but the " echo " template for a future test is created." echo exit 1 ;; esac fi ########################################################################## TEST_PREF=`echo $fname | sed s/\.test//` INUTREE=${TEST_PREF}.trees INCTREE=${TEST_PREF}.ctrees PARAMS=${TEST_PREF}.param # default DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees # # data type # case "$TEST_PREF" in *-nucl) TESTTYPE="${TESTTYPE}nucleotide data" DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees echo d > $PARAMS case "$TEST_PREF" in *-hky*) TESTTYPE="${TESTTYPE}, HKY" ;; *-tn*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS ;; *-gtr*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS echo m >> $PARAMS ;; *-sh*) TESTTYPE="${TESTTYPE}, SH" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-prot) TESTTYPE="${TESTTYPE}protein data" DATA=prot INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/globin.a INUTREESOURCE=../data/globin.trees INCTREESOURCE=../data/globin.ctrees echo d > $PARAMS echo d >> $PARAMS case "$TEST_PREF" in *-dayhoff*) TESTTYPE="${TESTTYPE}, Dayhoff" echo m >> $PARAMS ;; *-jtt*) TESTTYPE="${TESTTYPE}, JTT" echo m >> $PARAMS echo m >> $PARAMS ;; *-mtrev*) TESTTYPE="${TESTTYPE}, mtREV" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-blosum*) TESTTYPE="${TESTTYPE}, BLOSUM" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-vt*) TESTTYPE="${TESTTYPE}, VT" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-wag*) TESTTYPE="${TESTTYPE}, WAG" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-bin) TESTTYPE="${TESTTYPE}binary data" DATA=bin INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/primates.b INUTREESOURCE=../data/primates.trees INCTREESOURCE=../data/primates.ctrees echo d > $PARAMS echo d >> $PARAMS echo d >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}default data, default model" ;; esac case "$TEST_PREF" in *-clock*) TESTTYPE="${TESTTYPE}, clock" echo z >> $PARAMS ;; esac case "$TEST_PREF" in *-rhet4*) TESTTYPE="${TESTTYPE}, rate heterogeneity (4 rates)" echo w >> $PARAMS echo c >> $PARAMS echo 4 >> $PARAMS ;; *-rhet*) TESTTYPE="${TESTTYPE}, rate heterogeneity" echo w >> $PARAMS ;; esac CHECK_PREF=check-$INFILE case "$TEST_PREF" in qp-*) TESTTYPE="${TESTTYPE}, quartet puzzling" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; lm-*) TESTTYPE="${TESTTYPE}, likelihood mapping" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo b >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; ut-*) TESTTYPE="${TESTTYPE}, user tree evaluation" cp $INFILESOURCE $INFILE cp $INUTREESOURCE $INUTREE RESULT_PREF=$INUTREE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INUTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; cons-*) TESTTYPE="${TESTTYPE}, consensus construction" cp $INFILESOURCE $INFILE cp $INCTREESOURCE $INCTREE RESULT_PREF=$INCTREE echo k >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INCTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; *) echo; echo "$TESTTYPE ($TEST_PREF)" echo UNKNOWN analysis type: test ignored exit 77 ;; esac if test $GENERATE == 1; then cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > check-${TEST_PREF} exit 0 else cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? exit $result fi tree-puzzle-5.2/tests/generate-scripts.sh0000755000076400001440000000207210073365622014314 #! /bin/sh # # generate-scripts.sh # # # Part of TREE-PUZZLE 5.2 (July 2004) # # (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler # (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, # M. Vingron, and Arndt von Haeseler # (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler # # All parts of the source except where indicated are distributed under # the GNU public licence. See http://www.opensource.org for details. # # ($Id$) # QPSCRIPTS="\ qp-pure-bin.test\ qp-pure-nucl.test\ qp-tn-nucl.test\ qp-hky-clock-nucl.test\ qp-hky-rhet-nucl.test\ qp-hky-rhet-clock-nucl.test\ qp-pure-prot.test\ qp-mtrev-prot.test\ qp-vt-prot.test\ qp-wag-prot.test\ qp-clock.test\ qp-jtt-prot.test\ qp-jtt-rhet-prot.test\ qp-jtt-rhet-clock-prot.test\ " LMSCRIPT="\ lm-pure-prot.test\ " UTSCRIPTS="\ ut-pure-prot.test\ " UCSCRIPTS="\ cons-pure-prot.test\ " SCRIPTS="$QPSCRIPTS $LMSCRIPT $UTSCRIPTS $UCSCRIPTS" for i in $SCRIPTS ; do echo " $i" cp template-test $i chmod a+rx $i done tree-puzzle-5.2/tests/lm-pure-prot.test0000755000076400001440000001622410073365716013755 #! /bin/sh # # template-test # # # Part of TREE-PUZZLE 5.2 (July 2004) # # (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler # (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, # M. Vingron, and Arndt von Haeseler # (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler # # All parts of the source except where indicated are distributed under # the GNU public licence. See http://www.opensource.org for details. # # ($Id$) # fname=`echo $0 | sed 's/.*\///'` GENERATE=0 TESTTYPE="Testing: " if test 0 -ne $# then case "$1" in -g*) GENERATE=1 TESTTYPE="Generating: " ;; *) echo "Usage: $fname [-g] " echo echo " Test a TREE-PUZZLE scenario." echo " With -g no test is performed, but the " echo " template for a future test is created." echo exit 1 ;; esac fi ########################################################################## TEST_PREF=`echo $fname | sed s/\.test//` INUTREE=${TEST_PREF}.trees INCTREE=${TEST_PREF}.ctrees PARAMS=${TEST_PREF}.param # default DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees # # data type # case "$TEST_PREF" in *-nucl) TESTTYPE="${TESTTYPE}nucleotide data" DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees echo d > $PARAMS case "$TEST_PREF" in *-hky*) TESTTYPE="${TESTTYPE}, HKY" ;; *-tn*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS ;; *-gtr*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS echo m >> $PARAMS ;; *-sh*) TESTTYPE="${TESTTYPE}, SH" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-prot) TESTTYPE="${TESTTYPE}protein data" DATA=prot INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/globin.a INUTREESOURCE=../data/globin.trees INCTREESOURCE=../data/globin.ctrees echo d > $PARAMS echo d >> $PARAMS case "$TEST_PREF" in *-dayhoff*) TESTTYPE="${TESTTYPE}, Dayhoff" echo m >> $PARAMS ;; *-jtt*) TESTTYPE="${TESTTYPE}, JTT" echo m >> $PARAMS echo m >> $PARAMS ;; *-mtrev*) TESTTYPE="${TESTTYPE}, mtREV" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-blosum*) TESTTYPE="${TESTTYPE}, BLOSUM" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-vt*) TESTTYPE="${TESTTYPE}, VT" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-wag*) TESTTYPE="${TESTTYPE}, WAG" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-bin) TESTTYPE="${TESTTYPE}binary data" DATA=bin INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/primates.b INUTREESOURCE=../data/primates.trees INCTREESOURCE=../data/primates.ctrees echo d > $PARAMS echo d >> $PARAMS echo d >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}default data, default model" ;; esac case "$TEST_PREF" in *-clock*) TESTTYPE="${TESTTYPE}, clock" echo z >> $PARAMS ;; esac case "$TEST_PREF" in *-rhet4*) TESTTYPE="${TESTTYPE}, rate heterogeneity (4 rates)" echo w >> $PARAMS echo c >> $PARAMS echo 4 >> $PARAMS ;; *-rhet*) TESTTYPE="${TESTTYPE}, rate heterogeneity" echo w >> $PARAMS ;; esac CHECK_PREF=check-$INFILE case "$TEST_PREF" in qp-*) TESTTYPE="${TESTTYPE}, quartet puzzling" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; lm-*) TESTTYPE="${TESTTYPE}, likelihood mapping" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo b >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; ut-*) TESTTYPE="${TESTTYPE}, user tree evaluation" cp $INFILESOURCE $INFILE cp $INUTREESOURCE $INUTREE RESULT_PREF=$INUTREE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INUTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; cons-*) TESTTYPE="${TESTTYPE}, consensus construction" cp $INFILESOURCE $INFILE cp $INCTREESOURCE $INCTREE RESULT_PREF=$INCTREE echo k >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INCTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; *) echo; echo "$TESTTYPE ($TEST_PREF)" echo UNKNOWN analysis type: test ignored exit 77 ;; esac if test $GENERATE == 1; then cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > check-${TEST_PREF} exit 0 else cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? exit $result fi tree-puzzle-5.2/tests/check-qp-hky-rhet-nucl0000644000076400001440000002415010073365720014604 TREE-PUZZLE Input file name: qp-hky-rhet-nucl.nucl Type of analysis: tree reconstruction Parameter estimation: approximate (faster) Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) Standard errors (S.E.) are obtained by the curvature method. The upper and lower bounds of an approximate 95% confidence interval for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. SEQUENCE ALIGNMENT Input data: 8 sequences with 116 nucleotide sites Number of constant sites: 66 (= 56.9% of all sites) Number of site patterns: 54 Number of constant site patterns: 4 (= 7.4% of all site patterns) SUBSTITUTION PROCESS Model of substitution: HKY (Hasegawa et al. 1985) Transition/transversion parameter (estimated from data set): 2.95 (S.E. 0.84) Rate matrix R (parameters restricted to selected model): A-C rate: 1.00000 A-G rate: 5.85063 A-T rate: 1.00000 C-G rate: 1.00000 C-T rate: 5.85063 G-T rate: 1.00000 Nucleotide frequencies (estimated from data set): pi(A) = 26.6% pi(C) = 30.6% pi(G) = 12.0% pi(T) = 30.7% Expected transition/transversion ratio: 3.14 Expected pyrimidine transition/purine transition ratio: 2.95 AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) gaps wildcards sum % sequence Thylacinus 0 0 0 0.00% Sarcophilu 0 0 0 0.00% Dasyurus 0 1 1 0.86% Echymipera 0 0 0 0.00% Trichosuru 0 0 0 0.00% Phalanger 0 0 0 0.00% Philander 0 0 0 0.00% Bos 0 0 0 0.00% ------------------------------------------------------- Sum 0 1 1 0.11% The table above shows the amount of gaps ('-') and other 'wildcard' characters ('X', '?', etc.) and their percentage of the 116 columns in the alignment. Sequences with more than 50% ambiguous characters are marked with a '!' and should be checked, whether they have sufficient overlap to other sequences. Sequences with 100% ambiguous characters do not hold any phylogenetic information and had to be discarded from the analysis. SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) 5% chi-square test p-value Thylacinus passed 90.89% Sarcophilu passed 93.32% Dasyurus passed 98.01% Echymipera passed 92.83% Trichosuru passed 90.41% Phalanger passed 86.09% Philander passed 66.19% Bos passed 60.02% The chi-square tests compares the nucleotide composition of each sequence to the frequency distribution assumed in the maximum likelihood model. IDENTICAL SEQUENCES The sequences in each of the following groups are all identical. To speed up computation please remove all but one of each group from the data set. All sequences are unique. MAXIMUM LIKELIHOOD DISTANCES Maximum likelihood distances are computed using the selected model of substitution and rate heterogeneity. 8 Thylacinus 0.00000 0.52940 0.37900 0.52236 0.58922 0.56150 0.43932 0.55291 Sarcophilu 0.52940 0.00000 0.17837 0.62532 0.69892 0.93602 0.62327 0.78596 Dasyurus 0.37900 0.17837 0.00000 0.39032 0.53431 0.60369 0.31919 0.56220 Echymipera 0.52236 0.62532 0.39032 0.00000 0.70229 0.94283 0.42016 0.66063 Trichosuru 0.58922 0.69892 0.53431 0.70229 0.00000 0.39416 0.70017 0.62697 Phalanger 0.56150 0.93602 0.60369 0.94283 0.39416 0.00000 0.78658 0.98921 Philander 0.43932 0.62327 0.31919 0.42016 0.70017 0.78658 0.00000 0.49264 Bos 0.55291 0.78596 0.56220 0.66063 0.62697 0.98921 0.49264 0.00000 Average distance (over all possible pairs of sequences): 0.59096 minimum : 0.17837, maximum : 0.98921 variance : 0.03581, std.dev. : 0.18924 RATE HETEROGENEITY Model of rate heterogeneity: Gamma distributed rates Gamma distribution parameter alpha (estimated from data set): 0.25 (S.E. 0.05) Number of Gamma rate categories: 8 Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability 1 0.0000 0.1250 2 0.0031 0.1250 3 0.0262 0.1250 4 0.1071 0.1250 5 0.3140 0.1250 6 0.7768 0.1250 7 1.8180 0.1250 8 4.9547 0.1250 Categories 1-8 approximate a continous Gamma-distribution with expectation 1 and variance 3.94. Combination of categories that contributes the most to the likelihood (computation done without clock assumption assuming quartet-puzzling tree): 7 1 1 7 1 1 8 1 1 8 7 1 7 6 1 6 1 1 7 8 1 8 1 1 1 7 1 1 7 5 8 6 1 8 1 1 1 1 1 5 6 1 8 1 1 6 1 1 7 7 1 1 1 1 7 7 1 1 1 1 7 1 1 6 1 1 7 1 1 5 1 1 8 6 1 8 1 1 6 1 1 6 8 7 7 1 1 8 1 1 8 1 1 7 1 1 8 1 1 8 5 1 8 5 1 7 1 1 7 1 1 6 1 5 7 1 QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) name | resolved | partly resolved | unresolved | sum -------------------------------------------------------------------------- Thylacinus 15 [ 42.86%] 0 [ 0.00%] 20 [ 57.14%] 35 Sarcophilu 16 [ 45.71%] 1 [ 2.86%] 18 [ 51.43%] 35 Dasyurus 19 [ 54.29%] 3 [ 8.57%] 13 [ 37.14%] 35 Echymipera 12 [ 34.29%] 0 [ 0.00%] 23 [ 65.71%] 35 Trichosuru 16 [ 45.71%] 2 [ 5.71%] 17 [ 48.57%] 35 Phalanger 20 [ 57.14%] 2 [ 5.71%] 13 [ 37.14%] 35 Philander 13 [ 37.14%] 1 [ 2.86%] 21 [ 60.00%] 35 Bos 9 [ 25.71%] 3 [ 8.57%] 23 [ 65.71%] 35 -------------------------------------------------------------------------- #quartets : 30 [ 42.86%] 3 [ 4.29%] 37 [ 52.86%] 70 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage relative to the number of times the sequence occurs in the list of quartets (i.e. 35 quartets out of 70 in total). In fully resolved quartet one single topology is supported, while for partially resolved quartets two and for completely unresolved quartets none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. Note: Because 4 sequences are involved in one quartet numbers add up to a four-fold of the existing quartets. Hint: The overall numbers in the last row give information about the phylogenetic content of the dataset. The higher the percentage of partially and unresolved quartets, the lower the content of phylogenetic information. This can be visualized in more detail by likelihood mapping analysis. TREE SEARCH Quartet puzzling is used to choose from the possible tree topologies and to simultaneously infer support values for internal branches. Number of puzzling steps: 1000 Analysed quartets: 70 Fully resolved quartets: 30 (= 42.9%) Partly resolved quartets: 3 (= 4.3%) Unresolved quartets: 37 (= 52.9%) Quartet trees are based on approximate maximum likelihood values using the selected model of substitution and rate heterogeneity. QUARTET PUZZLING TREE Support for the internal branches of the unrooted quartet puzzling tree topology is shown in percent. This quartet puzzling tree is not completely resolved! :---Sarcophilu :-90: : :---Dasyurus : : :---Trichosuru :-87: : :---Phalanger : :-------Echymipera : :-------Philander : :-------Bos : :-------Thylacinus Quartet puzzling tree (in CLUSTAL W notation): (Thylacinus,(Sarcophilu,Dasyurus)90,(Trichosuru,Phalanger)87, Echymipera,Philander,Bos); BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) *..***** : 904 ****..** : 872 Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen) *...**.. : 377 ******.. : 357 Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen) ***.**.* : 220 ***.**.. : 218 *...**** : 205 ***.***. : 145 *......* : 135 *..*..** : 129 *...**.* : 124 *.....** : 106 *..*.... : 102 *..***.* : 92 *..***.. : 91 ***..... : 86 *.....*. : 71 ***...** : 70 *..****. : 67 ****..*. : 67 *....*.. : 64 *...***. : 54 ****.... : 52 *..*...* : 47 (49 other less frequent bipartitions not shown) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :------2 Sarcophilu :-------9 : :-3 Dasyurus : : :-----5 Trichosuru :-------10 : :--------6 Phalanger : :--------4 Echymipera : :-------7 Philander : :-----------8 Bos : :-------1 Thylacinus branch length S.E. branch length S.E. Thylacinus 1 0.23363 0.10248 9 0.19927 0.09576 Sarcophilu 2 0.18905 0.06712 10 0.22291 0.13093 Dasyurus 3 0.00001 0.00200 Echymipera 4 0.27841 0.11691 Trichosuru 5 0.17822 0.10160 Phalanger 6 0.27519 0.12613 Philander 7 0.22533 0.10269 10 iterations until convergence Bos 8 0.38507 0.14566 log L: -570.33 WARNING --- at least one branch length is close to an internal boundary! Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Thylacinus:0.23363,(Sarcophilu:0.18905,Dasyurus:0.00001)90:0.19927, (Trichosuru:0.17822,Phalanger:0.27519)87:0.22291,Echymipera:0.27841, Philander:0.22533,Bos:0.38507); TIME STAMP tree-puzzle-5.2/tests/check-qp-vt-prot0000644000076400001440000002060310073365722013526 TREE-PUZZLE Input file name: qp-vt-prot.prot Type of analysis: tree reconstruction Parameter estimation: approximate (faster) Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) Standard errors (S.E.) are obtained by the curvature method. The upper and lower bounds of an approximate 95% confidence interval for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. SEQUENCE ALIGNMENT Input data: 7 sequences with 128 amino acid sites Number of constant sites: 7 (= 5.5% of all sites) Number of site patterns: 125 Number of constant site patterns: 5 (= 4.0% of all site patterns) SUBSTITUTION PROCESS Model of substitution: VT (Mueller-Vingron 2000) Amino acid frequencies (estimated from data set): pi(A) = 12.2% pi(R) = 2.3% pi(N) = 3.0% pi(D) = 4.9% pi(C) = 0.7% pi(Q) = 2.3% pi(E) = 5.4% pi(G) = 6.0% pi(H) = 5.8% pi(I) = 2.7% pi(L) = 12.5% pi(K) = 9.3% pi(M) = 1.3% pi(F) = 4.9% pi(P) = 2.6% pi(S) = 6.7% pi(T) = 4.5% pi(W) = 1.3% pi(Y) = 2.2% pi(V) = 9.4% AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) gaps wildcards sum % sequence HBB_HUMAN 0 0 0 0.00% HBB_HORSE 0 0 0 0.00% HBA_HUMAN 0 0 0 0.00% HBA_HORSE 0 0 0 0.00% MYG_PHYCA 0 0 0 0.00% GLB5_PETMA 0 0 0 0.00% LGB2_LUPLU 0 0 0 0.00% ------------------------------------------------------- Sum 0 0 0 0.00% The table above shows the amount of gaps ('-') and other 'wildcard' characters ('X', '?', etc.) and their percentage of the 128 columns in the alignment. Sequences with more than 50% ambiguous characters are marked with a '!' and should be checked, whether they have sufficient overlap to other sequences. Sequences with 100% ambiguous characters do not hold any phylogenetic information and had to be discarded from the analysis. SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) 5% chi-square test p-value HBB_HUMAN passed 92.31% HBB_HORSE passed 79.58% HBA_HUMAN passed 93.09% HBA_HORSE passed 81.20% MYG_PHYCA passed 33.23% GLB5_PETMA passed 19.11% LGB2_LUPLU passed 41.67% The chi-square tests compares the amino acid composition of each sequence to the frequency distribution assumed in the maximum likelihood model. WARNING: Result of chi-square test may not be valid because of small maximum likelihood frequencies and short sequence length! IDENTICAL SEQUENCES The sequences in each of the following groups are all identical. To speed up computation please remove all but one of each group from the data set. All sequences are unique. MAXIMUM LIKELIHOOD DISTANCES Maximum likelihood distances are computed using the selected model of substitution and rate heterogeneity. 7 HBB_HUMAN 0.00000 0.16783 0.85204 0.87347 1.69056 1.50964 2.05575 HBB_HORSE 0.16783 0.00000 0.87363 0.87544 1.67978 1.52916 2.09374 HBA_HUMAN 0.85204 0.87363 0.00000 0.11958 1.58540 1.13053 2.11864 HBA_HORSE 0.87347 0.87544 0.11958 0.00000 1.64085 1.18694 2.01999 MYG_PHYCA 1.69056 1.67978 1.58540 1.64085 0.00000 1.63531 2.09093 GLB5_PETMA 1.50964 1.52916 1.13053 1.18694 1.63531 0.00000 1.84636 LGB2_LUPLU 2.05575 2.09374 2.11864 2.01999 2.09093 1.84636 0.00000 Average distance (over all possible pairs of sequences): 1.40836 minimum : 0.11958, maximum : 2.11864 variance : 0.36159, std.dev. : 0.60133 RATE HETEROGENEITY Model of rate heterogeneity: uniform rate QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) name | resolved | partly resolved | unresolved | sum -------------------------------------------------------------------------- HBB_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 HBB_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 HBA_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 HBA_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 MYG_PHYCA 16 [ 80.00%] 0 [ 0.00%] 4 [ 20.00%] 20 GLB5_PETMA 16 [ 80.00%] 0 [ 0.00%] 4 [ 20.00%] 20 LGB2_LUPLU 16 [ 80.00%] 0 [ 0.00%] 4 [ 20.00%] 20 -------------------------------------------------------------------------- #quartets : 31 [ 88.57%] 0 [ 0.00%] 4 [ 11.43%] 35 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage relative to the number of times the sequence occurs in the list of quartets (i.e. 20 quartets out of 35 in total). In fully resolved quartet one single topology is supported, while for partially resolved quartets two and for completely unresolved quartets none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. Note: Because 4 sequences are involved in one quartet numbers add up to a four-fold of the existing quartets. Hint: The overall numbers in the last row give information about the phylogenetic content of the dataset. The higher the percentage of partially and unresolved quartets, the lower the content of phylogenetic information. This can be visualized in more detail by likelihood mapping analysis. TREE SEARCH Quartet puzzling is used to choose from the possible tree topologies and to simultaneously infer support values for internal branches. Number of puzzling steps: 1000 Analysed quartets: 35 Fully resolved quartets: 31 (= 88.6%) Partly resolved quartets: 0 (= 0.0%) Unresolved quartets: 4 (= 11.4%) Quartet trees are based on approximate maximum likelihood values using the selected model of substitution and rate heterogeneity. QUARTET PUZZLING TREE Support for the internal branches of the unrooted quartet puzzling tree topology is shown in percent. This quartet puzzling tree is not completely resolved! :---MYG_PHYCA : :100:---GLB5_PETMA : : :100: :---LGB2_LUPLU : : : : :---HBA_HUMAN : :100: : :---HBA_HORSE : :-----------HBB_HORSE : :-----------HBB_HUMAN Quartet puzzling tree (in CLUSTAL W notation): (HBB_HUMAN,((MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)100,(HBA_HUMAN, HBA_HORSE)100)100,HBB_HORSE); BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) ****... : 1000 **..... : 1000 **..*** : 1000 Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen) *****.. : 347 Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen) ****..* : 331 ****.*. : 322 MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :-------------5 MYG_PHYCA :-------8 : :--------6 GLB5_PETMA : : : :------------------7 LGB2_LUPLU :-------10 : : :-3 HBA_HUMAN : :-----9 : :--4 HBA_HORSE : :--2 HBB_HORSE : :-1 HBB_HUMAN branch length S.E. branch length S.E. HBB_HUMAN 1 0.04599 0.03062 8 0.42025 0.11481 HBB_HORSE 2 0.12231 0.03740 9 0.25241 0.08069 HBA_HUMAN 3 0.03150 0.02213 10 0.54296 0.10035 HBA_HORSE 4 0.08803 0.03011 MYG_PHYCA 5 1.02811 0.16334 GLB5_PETMA 6 0.60661 0.11823 12 iterations until convergence LGB2_LUPLU 7 1.38558 0.20879 log L: -1703.59 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): (HBB_HUMAN:0.04599,((MYG_PHYCA:1.02811,GLB5_PETMA:0.60661,LGB2_LUPLU:1.38558) 100:0.42025,(HBA_HUMAN:0.03150,HBA_HORSE:0.08803)100:0.25241)100:0.54296, HBB_HORSE:0.12231); TIME STAMP tree-puzzle-5.2/tests/check-qp-hky-rhet-clock-nucl0000644000076400001440000003027010073365721015676 TREE-PUZZLE Input file name: qp-hky-rhet-clock-nucl.nucl Type of analysis: tree reconstruction Parameter estimation: approximate (faster) Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) Standard errors (S.E.) are obtained by the curvature method. The upper and lower bounds of an approximate 95% confidence interval for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. SEQUENCE ALIGNMENT Input data: 8 sequences with 116 nucleotide sites Number of constant sites: 66 (= 56.9% of all sites) Number of site patterns: 54 Number of constant site patterns: 4 (= 7.4% of all site patterns) SUBSTITUTION PROCESS Model of substitution: HKY (Hasegawa et al. 1985) Transition/transversion parameter (estimated from data set): 2.95 (S.E. 0.84) Rate matrix R (parameters restricted to selected model): A-C rate: 1.00000 A-G rate: 5.85063 A-T rate: 1.00000 C-G rate: 1.00000 C-T rate: 5.85063 G-T rate: 1.00000 Nucleotide frequencies (estimated from data set): pi(A) = 26.6% pi(C) = 30.6% pi(G) = 12.0% pi(T) = 30.7% Expected transition/transversion ratio: 3.14 Expected pyrimidine transition/purine transition ratio: 2.95 AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) gaps wildcards sum % sequence Thylacinus 0 0 0 0.00% Sarcophilu 0 0 0 0.00% Dasyurus 0 1 1 0.86% Echymipera 0 0 0 0.00% Trichosuru 0 0 0 0.00% Phalanger 0 0 0 0.00% Philander 0 0 0 0.00% Bos 0 0 0 0.00% ------------------------------------------------------- Sum 0 1 1 0.11% The table above shows the amount of gaps ('-') and other 'wildcard' characters ('X', '?', etc.) and their percentage of the 116 columns in the alignment. Sequences with more than 50% ambiguous characters are marked with a '!' and should be checked, whether they have sufficient overlap to other sequences. Sequences with 100% ambiguous characters do not hold any phylogenetic information and had to be discarded from the analysis. SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) 5% chi-square test p-value Thylacinus passed 90.89% Sarcophilu passed 93.32% Dasyurus passed 98.01% Echymipera passed 92.83% Trichosuru passed 90.41% Phalanger passed 86.09% Philander passed 66.19% Bos passed 60.02% The chi-square tests compares the nucleotide composition of each sequence to the frequency distribution assumed in the maximum likelihood model. IDENTICAL SEQUENCES The sequences in each of the following groups are all identical. To speed up computation please remove all but one of each group from the data set. All sequences are unique. MAXIMUM LIKELIHOOD DISTANCES Maximum likelihood distances are computed using the selected model of substitution and rate heterogeneity. 8 Thylacinus 0.00000 0.52940 0.37900 0.52236 0.58922 0.56150 0.43932 0.55291 Sarcophilu 0.52940 0.00000 0.17837 0.62532 0.69892 0.93602 0.62327 0.78596 Dasyurus 0.37900 0.17837 0.00000 0.39032 0.53431 0.60369 0.31919 0.56220 Echymipera 0.52236 0.62532 0.39032 0.00000 0.70229 0.94283 0.42016 0.66063 Trichosuru 0.58922 0.69892 0.53431 0.70229 0.00000 0.39416 0.70017 0.62697 Phalanger 0.56150 0.93602 0.60369 0.94283 0.39416 0.00000 0.78658 0.98921 Philander 0.43932 0.62327 0.31919 0.42016 0.70017 0.78658 0.00000 0.49264 Bos 0.55291 0.78596 0.56220 0.66063 0.62697 0.98921 0.49264 0.00000 Average distance (over all possible pairs of sequences): 0.59096 minimum : 0.17837, maximum : 0.98921 variance : 0.03581, std.dev. : 0.18924 RATE HETEROGENEITY Model of rate heterogeneity: Gamma distributed rates Gamma distribution parameter alpha (estimated from data set): 0.25 (S.E. 0.05) Number of Gamma rate categories: 8 Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability 1 0.0000 0.1250 2 0.0031 0.1250 3 0.0262 0.1250 4 0.1071 0.1250 5 0.3140 0.1250 6 0.7768 0.1250 7 1.8180 0.1250 8 4.9547 0.1250 Categories 1-8 approximate a continous Gamma-distribution with expectation 1 and variance 3.94. Combination of categories that contributes the most to the likelihood (computation done without clock assumption assuming quartet-puzzling tree): 7 1 1 7 1 1 8 1 1 8 7 1 7 6 1 6 1 1 7 8 1 8 1 1 1 7 1 1 7 5 8 6 1 8 1 1 1 1 1 5 6 1 8 1 1 6 1 1 7 7 1 1 1 1 7 7 1 1 1 1 7 1 1 6 1 1 7 1 1 5 1 1 8 6 1 8 1 1 6 1 1 6 8 7 7 1 1 8 1 1 8 1 1 7 1 1 8 1 1 8 5 1 8 5 1 7 1 1 7 1 1 6 1 5 7 1 QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) name | resolved | partly resolved | unresolved | sum -------------------------------------------------------------------------- Thylacinus 15 [ 42.86%] 0 [ 0.00%] 20 [ 57.14%] 35 Sarcophilu 16 [ 45.71%] 1 [ 2.86%] 18 [ 51.43%] 35 Dasyurus 19 [ 54.29%] 3 [ 8.57%] 13 [ 37.14%] 35 Echymipera 12 [ 34.29%] 0 [ 0.00%] 23 [ 65.71%] 35 Trichosuru 16 [ 45.71%] 2 [ 5.71%] 17 [ 48.57%] 35 Phalanger 20 [ 57.14%] 2 [ 5.71%] 13 [ 37.14%] 35 Philander 13 [ 37.14%] 1 [ 2.86%] 21 [ 60.00%] 35 Bos 9 [ 25.71%] 3 [ 8.57%] 23 [ 65.71%] 35 -------------------------------------------------------------------------- #quartets : 30 [ 42.86%] 3 [ 4.29%] 37 [ 52.86%] 70 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage relative to the number of times the sequence occurs in the list of quartets (i.e. 35 quartets out of 70 in total). In fully resolved quartet one single topology is supported, while for partially resolved quartets two and for completely unresolved quartets none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. Note: Because 4 sequences are involved in one quartet numbers add up to a four-fold of the existing quartets. Hint: The overall numbers in the last row give information about the phylogenetic content of the dataset. The higher the percentage of partially and unresolved quartets, the lower the content of phylogenetic information. This can be visualized in more detail by likelihood mapping analysis. TREE SEARCH Quartet puzzling is used to choose from the possible tree topologies and to simultaneously infer support values for internal branches. Number of puzzling steps: 1000 Analysed quartets: 70 Fully resolved quartets: 30 (= 42.9%) Partly resolved quartets: 3 (= 4.3%) Unresolved quartets: 37 (= 52.9%) Quartet trees are based on approximate maximum likelihood values using the selected model of substitution and rate heterogeneity. QUARTET PUZZLING TREE Support for the internal branches of the unrooted quartet puzzling tree topology is shown in percent. This quartet puzzling tree is not completely resolved! :---Sarcophilu :-90: : :---Dasyurus : : :---Trichosuru :-87: : :---Phalanger : :-------Echymipera : :-------Philander : :-------Bos : :-------Thylacinus Quartet puzzling tree (in CLUSTAL W notation): (Thylacinus,(Sarcophilu,Dasyurus)90,(Trichosuru,Phalanger)87, Echymipera,Philander,Bos); BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) *..***** : 904 ****..** : 872 Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen) *...**.. : 377 ******.. : 357 Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen) ***.**.* : 220 ***.**.. : 218 *...**** : 205 ***.***. : 145 *......* : 135 *..*..** : 129 *...**.* : 124 *.....** : 106 *..*.... : 102 *..***.* : 92 *..***.. : 91 ***..... : 86 *.....*. : 71 ***...** : 70 *..****. : 67 ****..*. : 67 *....*.. : 64 *...***. : 54 ****.... : 52 *..*...* : 47 (49 other less frequent bipartitions not shown) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :------2 Sarcophilu :-------9 : :-3 Dasyurus : : :-----5 Trichosuru :-------10 : :--------6 Phalanger : :--------4 Echymipera : :-------7 Philander : :-----------8 Bos : :-------1 Thylacinus branch length S.E. branch length S.E. Thylacinus 1 0.23363 0.10248 9 0.19927 0.09576 Sarcophilu 2 0.18905 0.06712 10 0.22291 0.13093 Dasyurus 3 0.00001 0.00200 Echymipera 4 0.27841 0.11691 Trichosuru 5 0.17822 0.10160 Phalanger 6 0.27519 0.12613 Philander 7 0.22533 0.10269 10 iterations until convergence Bos 8 0.38507 0.14566 log L: -570.33 WARNING --- at least one branch length is close to an internal boundary! Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Thylacinus:0.23363,(Sarcophilu:0.18905,Dasyurus:0.00001)90:0.19927, (Trichosuru:0.17822,Phalanger:0.27519)87:0.22291,Echymipera:0.27841, Philander:0.22533,Bos:0.38507); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF CONSENSUS TREE (WITH CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. Root located at branch: 10 "internal branch" (automatic search) If the automatic search misplaces the root please rerun the analysis (rename "outtree" to "intree") and select location of root manually! :---2 Sarcophilu :-------9 : :---3 Dasyurus : : :-------5 Trichosuru :-------10 : :-------6 Phalanger : :---------4 Echymipera : :---------7 Philander : :---------8 Bos : :---------1 Thylacinus Tree drawn as unrooted tree for better comparison with non-clock tree! branch length nc/c branch length nc/c (= non-clock/clock) Thylacinus 1 0.29776 0.785 9 0.20356 0.979 Sarcophilu 2 0.09420 2.007 10 0.22846 0.976 Dasyurus 3 0.09420 0.000 Echymipera 4 0.29776 0.935 Trichosuru 5 0.23472 0.759 Phalanger 6 0.23472 1.172 Philander 7 0.29776 0.757 16 iterations until convergence Bos 8 0.29776 1.293 log L: -573.89 height S.E. of node common to branches 0.23472 0.07631 10 5 6 0.09420 0.03153 9 2 3 0.29776 0.05401 10 4 7 8 1 9 0.38047 0.07031 of root at branch 10 Rooted consensus tree with clocklike maximum likelihood branch lengths (in CLUSTAL W notation): ((Trichosuru:0.23472,Phalanger:0.23472)87:0.14575,(Echymipera:0.29776, Philander:0.29776,Bos:0.29776,Thylacinus:0.29776,(Sarcophilu:0.09420, Dasyurus:0.09420)90:0.20356):0.08271); MOLECULAR CLOCK LIKELIHOOD RATIO TEST log L without clock: -570.33 (independent branch parameters: 10) log L with clock: -573.89 (independent branch parameters: 4) Likelihood ratio test statistic delta: 7.12 Degress of freedom of chi-square distribution: 6 Critical significance level: 30.97% The simpler (clocklike) tree can not be rejected on a significance level of 5%. The log-likelihood of the more complex (no clock) tree is not significantly increased. Please take care that the correct root is used! TIME STAMP tree-puzzle-5.2/tests/check-ut-pure-prot0000644000076400001440000002332210073365742014063 TREE-PUZZLE Input file name: ut-pure-prot.prot User tree file name: ut-pure-prot.trees Type of analysis: user tree evaluation Parameter estimation: approximate (faster) Parameter estimation uses: 1st user tree (for substitution process and rate variation) Standard errors (S.E.) are obtained by the curvature method. The upper and lower bounds of an approximate 95% confidence interval for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. SEQUENCE ALIGNMENT Input data: 7 sequences with 128 amino acid sites Number of constant sites: 7 (= 5.5% of all sites) Number of site patterns: 125 Number of constant site patterns: 5 (= 4.0% of all site patterns) SUBSTITUTION PROCESS Model of substitution: Dayhoff (Dayhoff et al. 1978) Amino acid frequencies (estimated from data set): pi(A) = 12.2% pi(R) = 2.3% pi(N) = 3.0% pi(D) = 4.9% pi(C) = 0.7% pi(Q) = 2.3% pi(E) = 5.4% pi(G) = 6.0% pi(H) = 5.8% pi(I) = 2.7% pi(L) = 12.5% pi(K) = 9.3% pi(M) = 1.3% pi(F) = 4.9% pi(P) = 2.6% pi(S) = 6.7% pi(T) = 4.5% pi(W) = 1.3% pi(Y) = 2.2% pi(V) = 9.4% AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) gaps wildcards sum % sequence HBB_HUMAN 0 0 0 0.00% HBB_HORSE 0 0 0 0.00% HBA_HUMAN 0 0 0 0.00% HBA_HORSE 0 0 0 0.00% MYG_PHYCA 0 0 0 0.00% GLB5_PETMA 0 0 0 0.00% LGB2_LUPLU 0 0 0 0.00% ------------------------------------------------------- Sum 0 0 0 0.00% The table above shows the amount of gaps ('-') and other 'wildcard' characters ('X', '?', etc.) and their percentage of the 128 columns in the alignment. Sequences with more than 50% ambiguous characters are marked with a '!' and should be checked, whether they have sufficient overlap to other sequences. Sequences with 100% ambiguous characters do not hold any phylogenetic information and had to be discarded from the analysis. SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) 5% chi-square test p-value HBB_HUMAN passed 92.31% HBB_HORSE passed 79.58% HBA_HUMAN passed 93.09% HBA_HORSE passed 81.20% MYG_PHYCA passed 33.23% GLB5_PETMA passed 19.11% LGB2_LUPLU passed 41.67% The chi-square tests compares the amino acid composition of each sequence to the frequency distribution assumed in the maximum likelihood model. WARNING: Result of chi-square test may not be valid because of small maximum likelihood frequencies and short sequence length! IDENTICAL SEQUENCES The sequences in each of the following groups are all identical. To speed up computation please remove all but one of each group from the data set. All sequences are unique. MAXIMUM LIKELIHOOD DISTANCES Maximum likelihood distances are computed using the selected model of substitution and rate heterogeneity. 7 HBB_HUMAN 0.00000 0.17425 0.96068 0.99267 2.12932 1.77231 2.78644 HBB_HORSE 0.17425 0.00000 1.01062 1.02118 2.09456 1.78465 2.86187 HBA_HUMAN 0.96068 1.01062 0.00000 0.12147 1.93540 1.30123 2.54730 HBA_HORSE 0.99267 1.02118 0.12147 0.00000 2.00515 1.39193 2.51172 MYG_PHYCA 2.12932 2.09456 1.93540 2.00515 0.00000 2.12347 2.79386 GLB5_PETMA 1.77231 1.78465 1.30123 1.39193 2.12347 0.00000 2.18272 LGB2_LUPLU 2.78644 2.86187 2.54730 2.51172 2.79386 2.18272 0.00000 Average distance (over all possible pairs of sequences): 1.73823 minimum : 0.12147, maximum : 2.86187 variance : 0.65214, std.dev. : 0.80755 RATE HETEROGENEITY Model of rate heterogeneity: uniform rate TREE SEARCH 4 tree topologies were specified by the user. MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 1 (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :--2 HBB_HORSE : : :-3 HBA_HUMAN : :----8 : : :-4 HBA_HORSE :------11 : : :-------------5 MYG_PHYCA : : :--9 : : : :-------6 GLB5_PETMA : :----10 : :-----------------7 LGB2_LUPLU : :-1 HBB_HUMAN branch length S.E. branch length S.E. HBB_HUMAN 1 0.04834 0.03148 8 0.28039 0.08746 HBB_HORSE 2 0.12686 0.03876 9 0.00001 0.00141 HBA_HUMAN 3 0.02653 0.02208 10 0.40361 0.12824 HBA_HORSE 4 0.09440 0.03145 11 0.60481 0.11282 MYG_PHYCA 5 1.33106 0.21114 GLB5_PETMA 6 0.70107 0.14140 9 iterations until convergence LGB2_LUPLU 7 1.76830 0.28198 log L: -1699.50 WARNING --- at least one branch length is close to an internal boundary! Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (HBB_HUMAN:0.04834,HBB_HORSE:0.12686,((HBA_HUMAN:0.02653,HBA_HORSE:0.09440) :0.28039,((MYG_PHYCA:1.33106,GLB5_PETMA:0.70107):0.00001,LGB2_LUPLU:1.76830) :0.40361):0.60481); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 2 (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :--2 HBB_HORSE : : :-3 HBA_HUMAN : :----8 : : :-4 HBA_HORSE :------11 : : :-------------5 MYG_PHYCA : :----10 : : :------6 GLB5_PETMA : :---9 : :----------------7 LGB2_LUPLU : :-1 HBB_HUMAN branch length S.E. branch length S.E. HBB_HUMAN 1 0.04915 0.03158 8 0.28347 0.08778 HBB_HORSE 2 0.12604 0.03871 9 0.18149 0.13088 HBA_HUMAN 3 0.02555 0.02185 10 0.34695 0.12552 HBA_HORSE 4 0.09541 0.03153 11 0.60238 0.11261 MYG_PHYCA 5 1.33157 0.21115 GLB5_PETMA 6 0.57473 0.13845 9 iterations until convergence LGB2_LUPLU 7 1.71340 0.27647 log L: -1699.00 Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (HBB_HUMAN:0.04915,HBB_HORSE:0.12604,((HBA_HUMAN:0.02555,HBA_HORSE:0.09541) :0.28347,(MYG_PHYCA:1.33157,(GLB5_PETMA:0.57473,LGB2_LUPLU:1.71340) :0.18149):0.34695):0.60238); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 3 (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :--2 HBB_HORSE : : :-3 HBA_HUMAN : :----8 : : :-4 HBA_HORSE :------11 : : :------------5 MYG_PHYCA : : :---9 : : : :----------------7 LGB2_LUPLU : :----10 : :-------6 GLB5_PETMA : :-1 HBB_HUMAN branch length S.E. branch length S.E. HBB_HUMAN 1 0.04869 0.03153 8 0.27871 0.08717 HBB_HORSE 2 0.12653 0.03874 9 0.12334 0.15661 HBA_HUMAN 3 0.02634 0.02204 10 0.39110 0.12780 HBA_HORSE 4 0.09459 0.03147 11 0.60627 0.11286 MYG_PHYCA 5 1.22880 0.20960 GLB5_PETMA 6 0.69972 0.14141 11 iterations until convergence LGB2_LUPLU 7 1.68480 0.28106 log L: -1699.32 Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (HBB_HUMAN:0.04869,HBB_HORSE:0.12653,((HBA_HUMAN:0.02634,HBA_HORSE:0.09459) :0.27871,((MYG_PHYCA:1.22880,LGB2_LUPLU:1.68480):0.12334,GLB5_PETMA:0.69972) :0.39110):0.60627); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 4 (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :-------------5 MYG_PHYCA :-----8 : :-------6 GLB5_PETMA : : : :-----------------7 LGB2_LUPLU :------10 : : :-3 HBA_HUMAN : :----9 : :-4 HBA_HORSE : :--2 HBB_HORSE : :-1 HBB_HUMAN branch length S.E. branch length S.E. HBB_HUMAN 1 0.04834 0.03148 8 0.40364 0.12824 HBB_HORSE 2 0.12685 0.03876 9 0.28040 0.08746 HBA_HUMAN 3 0.02653 0.02208 10 0.60481 0.11281 HBA_HORSE 4 0.09440 0.03145 MYG_PHYCA 5 1.33095 0.21112 GLB5_PETMA 6 0.70107 0.14140 10 iterations until convergence LGB2_LUPLU 7 1.76831 0.28198 log L: -1699.50 Unrooted user defined tree with maximum likelihood branch lengths (in CLUSTAL W notation): (HBB_HUMAN:0.04834,((MYG_PHYCA:1.33095,GLB5_PETMA:0.70107,LGB2_LUPLU:1.76831) :0.40364,(HBA_HUMAN:0.02653,HBA_HORSE:0.09440):0.28040):0.60481,HBB_HORSE:0.12685); COMPARISON OF USER TREES (NO CLOCK) Tree log L difference S.E. p-1sKH p-SH c-ELW 2sKH ------------------------------------------------------------------------------- 1 -1699.50 0.49 1.0266 0.3020 + 0.4700 + 0.1881 + + 2 -1699.00 0.00 <---- best 1.0000 + 1.0000 + 0.3650 + best 3 -1699.32 0.32 1.3440 0.4030 + 0.4690 + 0.2588 + + 4 -1699.50 0.49 1.0267 0.3070 + 0.4700 + 0.1881 + + The columns show the results and p-values of the following tests: 1sKH - one sided KH test based on pairwise SH tests (Shimodaira-Hasegawa 2000, Goldman et al., 2001, Kishino-Hasegawa 1989) SH - Shimodaira-Hasegawa test (2000) ELW - Expected Likelihood Weight (Strimmer-Rambaut 2002) 2sKH - two sided Kishino-Hasegawa test (1989) Plus signs denote the confidence sets. Minus signs denote significant exclusion. All tests used 5% significance level. 1sKH, SH, and ELW performed 1000 resamplings using the RELL method. 1sKH and 2sKH are correct to the 2nd position after the the decimal point of the log-likelihoods. TIME STAMP tree-puzzle-5.2/tests/qp-pure-prot.test0000755000076400001440000001622410073365716013765 #! /bin/sh # # template-test # # # Part of TREE-PUZZLE 5.2 (July 2004) # # (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler # (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, # M. Vingron, and Arndt von Haeseler # (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler # # All parts of the source except where indicated are distributed under # the GNU public licence. See http://www.opensource.org for details. # # ($Id$) # fname=`echo $0 | sed 's/.*\///'` GENERATE=0 TESTTYPE="Testing: " if test 0 -ne $# then case "$1" in -g*) GENERATE=1 TESTTYPE="Generating: " ;; *) echo "Usage: $fname [-g] " echo echo " Test a TREE-PUZZLE scenario." echo " With -g no test is performed, but the " echo " template for a future test is created." echo exit 1 ;; esac fi ########################################################################## TEST_PREF=`echo $fname | sed s/\.test//` INUTREE=${TEST_PREF}.trees INCTREE=${TEST_PREF}.ctrees PARAMS=${TEST_PREF}.param # default DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees # # data type # case "$TEST_PREF" in *-nucl) TESTTYPE="${TESTTYPE}nucleotide data" DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees echo d > $PARAMS case "$TEST_PREF" in *-hky*) TESTTYPE="${TESTTYPE}, HKY" ;; *-tn*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS ;; *-gtr*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS echo m >> $PARAMS ;; *-sh*) TESTTYPE="${TESTTYPE}, SH" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-prot) TESTTYPE="${TESTTYPE}protein data" DATA=prot INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/globin.a INUTREESOURCE=../data/globin.trees INCTREESOURCE=../data/globin.ctrees echo d > $PARAMS echo d >> $PARAMS case "$TEST_PREF" in *-dayhoff*) TESTTYPE="${TESTTYPE}, Dayhoff" echo m >> $PARAMS ;; *-jtt*) TESTTYPE="${TESTTYPE}, JTT" echo m >> $PARAMS echo m >> $PARAMS ;; *-mtrev*) TESTTYPE="${TESTTYPE}, mtREV" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-blosum*) TESTTYPE="${TESTTYPE}, BLOSUM" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-vt*) TESTTYPE="${TESTTYPE}, VT" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-wag*) TESTTYPE="${TESTTYPE}, WAG" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-bin) TESTTYPE="${TESTTYPE}binary data" DATA=bin INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/primates.b INUTREESOURCE=../data/primates.trees INCTREESOURCE=../data/primates.ctrees echo d > $PARAMS echo d >> $PARAMS echo d >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}default data, default model" ;; esac case "$TEST_PREF" in *-clock*) TESTTYPE="${TESTTYPE}, clock" echo z >> $PARAMS ;; esac case "$TEST_PREF" in *-rhet4*) TESTTYPE="${TESTTYPE}, rate heterogeneity (4 rates)" echo w >> $PARAMS echo c >> $PARAMS echo 4 >> $PARAMS ;; *-rhet*) TESTTYPE="${TESTTYPE}, rate heterogeneity" echo w >> $PARAMS ;; esac CHECK_PREF=check-$INFILE case "$TEST_PREF" in qp-*) TESTTYPE="${TESTTYPE}, quartet puzzling" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; lm-*) TESTTYPE="${TESTTYPE}, likelihood mapping" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo b >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; ut-*) TESTTYPE="${TESTTYPE}, user tree evaluation" cp $INFILESOURCE $INFILE cp $INUTREESOURCE $INUTREE RESULT_PREF=$INUTREE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INUTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; cons-*) TESTTYPE="${TESTTYPE}, consensus construction" cp $INFILESOURCE $INFILE cp $INCTREESOURCE $INCTREE RESULT_PREF=$INCTREE echo k >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INCTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; *) echo; echo "$TESTTYPE ($TEST_PREF)" echo UNKNOWN analysis type: test ignored exit 77 ;; esac if test $GENERATE == 1; then cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > check-${TEST_PREF} exit 0 else cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? exit $result fi tree-puzzle-5.2/tests/qp-tn-nucl.test0000755000076400001440000001622410073365716013410 #! /bin/sh # # template-test # # # Part of TREE-PUZZLE 5.2 (July 2004) # # (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler # (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, # M. Vingron, and Arndt von Haeseler # (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler # # All parts of the source except where indicated are distributed under # the GNU public licence. See http://www.opensource.org for details. # # ($Id$) # fname=`echo $0 | sed 's/.*\///'` GENERATE=0 TESTTYPE="Testing: " if test 0 -ne $# then case "$1" in -g*) GENERATE=1 TESTTYPE="Generating: " ;; *) echo "Usage: $fname [-g] " echo echo " Test a TREE-PUZZLE scenario." echo " With -g no test is performed, but the " echo " template for a future test is created." echo exit 1 ;; esac fi ########################################################################## TEST_PREF=`echo $fname | sed s/\.test//` INUTREE=${TEST_PREF}.trees INCTREE=${TEST_PREF}.ctrees PARAMS=${TEST_PREF}.param # default DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees # # data type # case "$TEST_PREF" in *-nucl) TESTTYPE="${TESTTYPE}nucleotide data" DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees echo d > $PARAMS case "$TEST_PREF" in *-hky*) TESTTYPE="${TESTTYPE}, HKY" ;; *-tn*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS ;; *-gtr*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS echo m >> $PARAMS ;; *-sh*) TESTTYPE="${TESTTYPE}, SH" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-prot) TESTTYPE="${TESTTYPE}protein data" DATA=prot INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/globin.a INUTREESOURCE=../data/globin.trees INCTREESOURCE=../data/globin.ctrees echo d > $PARAMS echo d >> $PARAMS case "$TEST_PREF" in *-dayhoff*) TESTTYPE="${TESTTYPE}, Dayhoff" echo m >> $PARAMS ;; *-jtt*) TESTTYPE="${TESTTYPE}, JTT" echo m >> $PARAMS echo m >> $PARAMS ;; *-mtrev*) TESTTYPE="${TESTTYPE}, mtREV" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-blosum*) TESTTYPE="${TESTTYPE}, BLOSUM" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-vt*) TESTTYPE="${TESTTYPE}, VT" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-wag*) TESTTYPE="${TESTTYPE}, WAG" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-bin) TESTTYPE="${TESTTYPE}binary data" DATA=bin INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/primates.b INUTREESOURCE=../data/primates.trees INCTREESOURCE=../data/primates.ctrees echo d > $PARAMS echo d >> $PARAMS echo d >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}default data, default model" ;; esac case "$TEST_PREF" in *-clock*) TESTTYPE="${TESTTYPE}, clock" echo z >> $PARAMS ;; esac case "$TEST_PREF" in *-rhet4*) TESTTYPE="${TESTTYPE}, rate heterogeneity (4 rates)" echo w >> $PARAMS echo c >> $PARAMS echo 4 >> $PARAMS ;; *-rhet*) TESTTYPE="${TESTTYPE}, rate heterogeneity" echo w >> $PARAMS ;; esac CHECK_PREF=check-$INFILE case "$TEST_PREF" in qp-*) TESTTYPE="${TESTTYPE}, quartet puzzling" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; lm-*) TESTTYPE="${TESTTYPE}, likelihood mapping" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo b >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; ut-*) TESTTYPE="${TESTTYPE}, user tree evaluation" cp $INFILESOURCE $INFILE cp $INUTREESOURCE $INUTREE RESULT_PREF=$INUTREE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INUTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; cons-*) TESTTYPE="${TESTTYPE}, consensus construction" cp $INFILESOURCE $INFILE cp $INCTREESOURCE $INCTREE RESULT_PREF=$INCTREE echo k >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INCTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; *) echo; echo "$TESTTYPE ($TEST_PREF)" echo UNKNOWN analysis type: test ignored exit 77 ;; esac if test $GENERATE == 1; then cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > check-${TEST_PREF} exit 0 else cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? exit $result fi tree-puzzle-5.2/tests/Makefile.am0000644000076400001440000000442310073365642012536 # # Makefile.am # # # Part of TREE-PUZZLE 5.2 (July 2004) # # (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler # (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, # M. Vingron, and Arndt von Haeseler # (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler # # All parts of the source except where indicated are distributed under # the GNU public licence. See http://www.opensource.org for details. # # ($Id$) # # Be sure to reexport important environment variables. TESTS_ENVIRONMENT = MAKE="$(MAKE)" CC="$(CC)" CFLAGS="$(CFLAGS)" \ CPPFLAGS="$(CPPFLAGS)" LD="$(LD)" LDFLAGS="$(LDFLAGS)" \ LIBS="$(LIBS)" LN_S="$(LN_S)" NM="$(NM)" RANLIB="$(RANLIB)" \ EXEEXT="$(EXEEXT)" PACKAGE="$(PACKAGE)" VERSION="$(VERSION)" TESTFILES = \ qp-pure-bin.test\ qp-pure-nucl.test\ qp-tn-nucl.test\ qp-hky-clock-nucl.test\ qp-hky-rhet-nucl.test\ qp-hky-rhet-clock-nucl.test\ qp-pure-prot.test\ qp-mtrev-prot.test\ qp-vt-prot.test\ qp-wag-prot.test\ qp-clock.test\ qp-jtt-prot.test\ qp-jtt-rhet-prot.test\ qp-jtt-rhet-clock-prot.test\ lm-pure-prot.test\ ut-pure-prot.test\ cons-pure-prot.test TESTS =\ build-puzzle\ $(TESTFILES)\ build-remark EXTRA_DIST = generate-scripts.sh template-test build-puzzle build-remark \ $(TESTFILES)\ check-qp-pure-bin\ check-qp-pure-nucl\ check-qp-tn-nucl\ check-qp-hky-clock-nucl\ check-qp-hky-rhet-nucl\ check-qp-hky-rhet-clock-nucl\ check-qp-pure-prot\ check-qp-jtt-prot\ check-qp-mtrev-prot\ check-qp-vt-prot\ check-qp-wag-prot\ check-qp-clock\ check-qp-jtt-rhet-prot\ check-qp-jtt-rhet-clock-prot\ check-lm-pure-prot\ check-ut-pure-prot\ check-cons-pure-prot build-puzzle: $(top_builddir)/src/puzzle build-remark: $(top_builddir)/src/puzzle: cd $(top_builddir) && $(MAKE) all generate: VERSION="$(VERSION)"; export VERSION; \ if test -x generate-scripts.sh -a -f template-test; then \ echo "generating test scripts:"; \ ./generate-scripts.sh; \ fi; \ echo "generating check files:"; \ for testprog in $(TESTS); do \ if test -x ./$$testprog ; then \ ./$$testprog -g; \ fi; \ done clean: rm -f *.param rm -f *.nucl *.prot *.bin *.trees *.ctrees rm -f *.nucl.* *.prot.* *.bin.* *.trees.* *.ctrees.* tree-puzzle-5.2/tests/Makefile.in0000644000076400001440000002206010075305510012532 # Makefile.in generated by automake 1.6.1 from Makefile.am. # @configure_input@ # Copyright 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002 # Free Software Foundation, Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, # with or without modifications, as long as this notice is preserved. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY, to the extent permitted by law; without # even the implied warranty of MERCHANTABILITY or FITNESS FOR A # PARTICULAR PURPOSE. @SET_MAKE@ # # Makefile.am # # # Part of TREE-PUZZLE 5.2 (July 2004) # # (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler # (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, # M. Vingron, and Arndt von Haeseler # (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler # # All parts of the source except where indicated are distributed under # the GNU public licence. See http://www.opensource.org for details. # # ($Id$) # SHELL = @SHELL@ srcdir = @srcdir@ top_srcdir = @top_srcdir@ VPATH = @srcdir@ prefix = @prefix@ exec_prefix = @exec_prefix@ bindir = @bindir@ sbindir = @sbindir@ libexecdir = @libexecdir@ datadir = @datadir@ sysconfdir = @sysconfdir@ sharedstatedir = @sharedstatedir@ localstatedir = @localstatedir@ libdir = @libdir@ infodir = @infodir@ mandir = @mandir@ includedir = @includedir@ oldincludedir = /usr/include pkgdatadir = $(datadir)/@PACKAGE@ pkglibdir = $(libdir)/@PACKAGE@ pkgincludedir = $(includedir)/@PACKAGE@ top_builddir = .. ACLOCAL = @ACLOCAL@ AUTOCONF = @AUTOCONF@ AUTOMAKE = @AUTOMAKE@ AUTOHEADER = @AUTOHEADER@ am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd INSTALL = @INSTALL@ INSTALL_PROGRAM = @INSTALL_PROGRAM@ INSTALL_DATA = @INSTALL_DATA@ install_sh_DATA = $(install_sh) -c -m 644 install_sh_PROGRAM = $(install_sh) -c INSTALL_SCRIPT = @INSTALL_SCRIPT@ INSTALL_HEADER = $(INSTALL_DATA) transform = @program_transform_name@ NORMAL_INSTALL = : PRE_INSTALL = : POST_INSTALL = : NORMAL_UNINSTALL = : PRE_UNINSTALL = : POST_UNINSTALL = : EXEEXT = @EXEEXT@ OBJEXT = @OBJEXT@ PATH_SEPARATOR = @PATH_SEPARATOR@ AMTAR = @AMTAR@ AWK = @AWK@ CC = @CC@ DEPDIR = @DEPDIR@ INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@ MPICC = @MPICC@ MPICC0 = @MPICC0@ MPICC1 = @MPICC1@ MPICC2 = @MPICC2@ MPICC3 = @MPICC3@ MPICC4 = @MPICC4@ MPICC5 = @MPICC5@ MPICC6 = @MPICC6@ MPICFLAGS = @MPICFLAGS@ MPIDEFS = @MPIDEFS@ MPILIBS = @MPILIBS@ PACKAGE = @PACKAGE@ PPUZZLE = @PPUZZLE@ STRIP = @STRIP@ VERSION = @VERSION@ am__include = @am__include@ am__quote = @am__quote@ install_sh = @install_sh@ # Be sure to reexport important environment variables. TESTS_ENVIRONMENT = MAKE="$(MAKE)" CC="$(CC)" CFLAGS="$(CFLAGS)" \ CPPFLAGS="$(CPPFLAGS)" LD="$(LD)" LDFLAGS="$(LDFLAGS)" \ LIBS="$(LIBS)" LN_S="$(LN_S)" NM="$(NM)" RANLIB="$(RANLIB)" \ EXEEXT="$(EXEEXT)" PACKAGE="$(PACKAGE)" VERSION="$(VERSION)" TESTFILES = \ qp-pure-bin.test\ qp-pure-nucl.test\ qp-tn-nucl.test\ qp-hky-clock-nucl.test\ qp-hky-rhet-nucl.test\ qp-hky-rhet-clock-nucl.test\ qp-pure-prot.test\ qp-mtrev-prot.test\ qp-vt-prot.test\ qp-wag-prot.test\ qp-clock.test\ qp-jtt-prot.test\ qp-jtt-rhet-prot.test\ qp-jtt-rhet-clock-prot.test\ lm-pure-prot.test\ ut-pure-prot.test\ cons-pure-prot.test TESTS = \ build-puzzle\ $(TESTFILES)\ build-remark EXTRA_DIST = generate-scripts.sh template-test build-puzzle build-remark \ $(TESTFILES)\ check-qp-pure-bin\ check-qp-pure-nucl\ check-qp-tn-nucl\ check-qp-hky-clock-nucl\ check-qp-hky-rhet-nucl\ check-qp-hky-rhet-clock-nucl\ check-qp-pure-prot\ check-qp-jtt-prot\ check-qp-mtrev-prot\ check-qp-vt-prot\ check-qp-wag-prot\ check-qp-clock\ check-qp-jtt-rhet-prot\ check-qp-jtt-rhet-clock-prot\ check-lm-pure-prot\ check-ut-pure-prot\ check-cons-pure-prot subdir = tests mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs CONFIG_HEADER = $(top_builddir)/src/config.h CONFIG_CLEAN_FILES = DIST_SOURCES = DIST_COMMON = Makefile.am Makefile.in all: all-am .SUFFIXES: $(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.ac $(ACLOCAL_M4) cd $(top_srcdir) && \ $(AUTOMAKE) --gnu tests/Makefile Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe) uninstall-info-am: tags: TAGS TAGS: check-TESTS: $(TESTS) @failed=0; all=0; xfail=0; xpass=0; \ srcdir=$(srcdir); export srcdir; \ list='$(TESTS)'; \ if test -n "$$list"; then \ for tst in $$list; do \ if test -f ./$$tst; then dir=./; \ elif test -f $$tst; then dir=; \ else dir="$(srcdir)/"; fi; \ if $(TESTS_ENVIRONMENT) $${dir}$$tst; then \ all=`expr $$all + 1`; \ case " $(XFAIL_TESTS) " in \ *" $$tst "*) \ xpass=`expr $$xpass + 1`; \ failed=`expr $$failed + 1`; \ echo "XPASS: $$tst"; \ ;; \ *) \ echo "PASS: $$tst"; \ ;; \ esac; \ elif test $$? 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The upper and lower bounds of an approximate 95% confidence interval for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. SEQUENCE ALIGNMENT Input data: 7 sequences with 128 amino acid sites Number of constant sites: 7 (= 5.5% of all sites) Number of site patterns: 125 Number of constant site patterns: 5 (= 4.0% of all site patterns) SUBSTITUTION PROCESS Model of substitution: JTT (Jones et al. 1992) Amino acid frequencies (estimated from data set): pi(A) = 12.2% pi(R) = 2.3% pi(N) = 3.0% pi(D) = 4.9% pi(C) = 0.7% pi(Q) = 2.3% pi(E) = 5.4% pi(G) = 6.0% pi(H) = 5.8% pi(I) = 2.7% pi(L) = 12.5% pi(K) = 9.3% pi(M) = 1.3% pi(F) = 4.9% pi(P) = 2.6% pi(S) = 6.7% pi(T) = 4.5% pi(W) = 1.3% pi(Y) = 2.2% pi(V) = 9.4% AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) gaps wildcards sum % sequence HBB_HUMAN 0 0 0 0.00% HBB_HORSE 0 0 0 0.00% HBA_HUMAN 0 0 0 0.00% HBA_HORSE 0 0 0 0.00% MYG_PHYCA 0 0 0 0.00% GLB5_PETMA 0 0 0 0.00% LGB2_LUPLU 0 0 0 0.00% ------------------------------------------------------- Sum 0 0 0 0.00% The table above shows the amount of gaps ('-') and other 'wildcard' characters ('X', '?', etc.) and their percentage of the 128 columns in the alignment. Sequences with more than 50% ambiguous characters are marked with a '!' and should be checked, whether they have sufficient overlap to other sequences. Sequences with 100% ambiguous characters do not hold any phylogenetic information and had to be discarded from the analysis. SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) 5% chi-square test p-value HBB_HUMAN passed 92.31% HBB_HORSE passed 79.58% HBA_HUMAN passed 93.09% HBA_HORSE passed 81.20% MYG_PHYCA passed 33.23% GLB5_PETMA passed 19.11% LGB2_LUPLU passed 41.67% The chi-square tests compares the amino acid composition of each sequence to the frequency distribution assumed in the maximum likelihood model. WARNING: Result of chi-square test may not be valid because of small maximum likelihood frequencies and short sequence length! IDENTICAL SEQUENCES The sequences in each of the following groups are all identical. To speed up computation please remove all but one of each group from the data set. All sequences are unique. MAXIMUM LIKELIHOOD DISTANCES Maximum likelihood distances are computed using the selected model of substitution and rate heterogeneity. 7 HBB_HUMAN 0.00000 0.17887 1.04805 1.08480 2.52050 2.10945 3.26098 HBB_HORSE 0.17887 0.00000 1.09690 1.10752 2.49215 2.12870 3.34229 HBA_HUMAN 1.04805 1.09690 0.00000 0.12538 2.35997 1.45565 3.24727 HBA_HORSE 1.08480 1.10752 0.12538 0.00000 2.43814 1.57611 3.14845 MYG_PHYCA 2.52050 2.49215 2.35997 2.43814 0.00000 2.54103 3.42222 GLB5_PETMA 2.10945 2.12870 1.45565 1.57611 2.54103 0.00000 2.84131 LGB2_LUPLU 3.26098 3.34229 3.24727 3.14845 3.42222 2.84131 0.00000 Average distance (over all possible pairs of sequences): 2.07265 minimum : 0.12538, maximum : 3.42222 variance : 1.03523, std.dev. : 1.01746 RATE HETEROGENEITY Model of rate heterogeneity: Gamma distributed rates Gamma distribution parameter alpha (estimated from data set): 2.85 (S.E. 1.58) Number of Gamma rate categories: 8 Rates and their respective probabilities used in the likelihood function: Category Relative rate Probability 1 0.2882 0.1250 2 0.4879 0.1250 3 0.6513 0.1250 4 0.8135 0.1250 5 0.9910 0.1250 6 1.2042 0.1250 7 1.4978 0.1250 8 2.0662 0.1250 Categories 1-8 approximate a continous Gamma-distribution with expectation 1 and variance 0.35. Combination of categories that contributes the most to the likelihood (computation done without clock assumption assuming quartet-puzzling tree): 8 1 1 8 3 2 6 4 8 1 8 2 4 1 8 4 1 8 8 8 6 6 1 8 3 3 1 4 1 6 2 8 5 8 1 8 1 4 4 7 1 8 8 1 4 2 1 6 6 1 4 4 2 2 8 1 2 7 3 1 8 8 2 5 8 8 2 4 8 4 8 3 7 6 8 8 7 1 4 8 1 1 7 8 1 2 8 1 7 6 1 1 8 1 1 6 4 2 5 7 4 1 6 8 1 2 4 8 7 4 1 5 8 6 2 8 6 6 8 3 6 6 7 2 6 4 3 1 QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) name | resolved | partly resolved | unresolved | sum -------------------------------------------------------------------------- HBB_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 HBB_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 HBA_HUMAN 19 [ 95.00%] 1 [ 5.00%] 0 [ 0.00%] 20 HBA_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 MYG_PHYCA 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 GLB5_PETMA 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 LGB2_LUPLU 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 -------------------------------------------------------------------------- #quartets : 31 [ 88.57%] 1 [ 2.86%] 3 [ 8.57%] 35 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage relative to the number of times the sequence occurs in the list of quartets (i.e. 20 quartets out of 35 in total). In fully resolved quartet one single topology is supported, while for partially resolved quartets two and for completely unresolved quartets none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. Note: Because 4 sequences are involved in one quartet numbers add up to a four-fold of the existing quartets. Hint: The overall numbers in the last row give information about the phylogenetic content of the dataset. The higher the percentage of partially and unresolved quartets, the lower the content of phylogenetic information. This can be visualized in more detail by likelihood mapping analysis. TREE SEARCH Quartet puzzling is used to choose from the possible tree topologies and to simultaneously infer support values for internal branches. Number of puzzling steps: 1000 Analysed quartets: 35 Fully resolved quartets: 31 (= 88.6%) Partly resolved quartets: 1 (= 2.9%) Unresolved quartets: 3 (= 8.6%) Quartet trees are based on approximate maximum likelihood values using the selected model of substitution and rate heterogeneity. QUARTET PUZZLING TREE Support for the internal branches of the unrooted quartet puzzling tree topology is shown in percent. This quartet puzzling tree is not completely resolved! :---MYG_PHYCA : :100:---GLB5_PETMA : : :100: :---LGB2_LUPLU : : : : :---HBA_HUMAN : :100: : :---HBA_HORSE : :-----------HBB_HORSE : :-----------HBB_HUMAN Quartet puzzling tree (in CLUSTAL W notation): (HBB_HUMAN,((MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)100,(HBA_HUMAN, HBA_HORSE)100)100,HBB_HORSE); BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) ****... : 1000 **..... : 1000 **..*** : 1000 Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen) *****.. : 393 Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen) ****.*. : 380 ****..* : 227 MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :--------------5 MYG_PHYCA :-----8 : :-------6 GLB5_PETMA : : : :-------------------7 LGB2_LUPLU :------10 : : :-3 HBA_HUMAN : :---9 : :-4 HBA_HORSE : :--2 HBB_HORSE : :-1 HBB_HUMAN branch length S.E. branch length S.E. HBB_HUMAN 1 0.04933 0.03409 8 0.50700 0.17281 HBB_HORSE 2 0.12953 0.04093 9 0.23403 0.10586 HBA_HUMAN 3 0.01995 0.02303 10 0.74732 0.14235 HBA_HORSE 4 0.10548 0.03367 MYG_PHYCA 5 1.68057 0.30228 GLB5_PETMA 6 0.81182 0.18641 12 iterations until convergence LGB2_LUPLU 7 2.33484 0.42478 log L: -1701.69 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): (HBB_HUMAN:0.04933,((MYG_PHYCA:1.68057,GLB5_PETMA:0.81182,LGB2_LUPLU:2.33484) 100:0.50700,(HBA_HUMAN:0.01995,HBA_HORSE:0.10548)100:0.23403)100:0.74732, HBB_HORSE:0.12953); TIME STAMP tree-puzzle-5.2/tests/qp-jtt-rhet-clock-prot.test0000755000076400001440000001622410073365716015644 #! /bin/sh # # template-test # # # Part of TREE-PUZZLE 5.2 (July 2004) # # (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler # (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, # M. Vingron, and Arndt von Haeseler # (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler # # All parts of the source except where indicated are distributed under # the GNU public licence. See http://www.opensource.org for details. # # ($Id$) # fname=`echo $0 | sed 's/.*\///'` GENERATE=0 TESTTYPE="Testing: " if test 0 -ne $# then case "$1" in -g*) GENERATE=1 TESTTYPE="Generating: " ;; *) echo "Usage: $fname [-g] " echo echo " Test a TREE-PUZZLE scenario." echo " With -g no test is performed, but the " echo " template for a future test is created." echo exit 1 ;; esac fi ########################################################################## TEST_PREF=`echo $fname | sed s/\.test//` INUTREE=${TEST_PREF}.trees INCTREE=${TEST_PREF}.ctrees PARAMS=${TEST_PREF}.param # default DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees # # data type # case "$TEST_PREF" in *-nucl) TESTTYPE="${TESTTYPE}nucleotide data" DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees echo d > $PARAMS case "$TEST_PREF" in *-hky*) TESTTYPE="${TESTTYPE}, HKY" ;; *-tn*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS ;; *-gtr*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS echo m >> $PARAMS ;; *-sh*) TESTTYPE="${TESTTYPE}, SH" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-prot) TESTTYPE="${TESTTYPE}protein data" DATA=prot INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/globin.a INUTREESOURCE=../data/globin.trees INCTREESOURCE=../data/globin.ctrees echo d > $PARAMS echo d >> $PARAMS case "$TEST_PREF" in *-dayhoff*) TESTTYPE="${TESTTYPE}, Dayhoff" echo m >> $PARAMS ;; *-jtt*) TESTTYPE="${TESTTYPE}, JTT" echo m >> $PARAMS echo m >> $PARAMS ;; *-mtrev*) TESTTYPE="${TESTTYPE}, mtREV" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-blosum*) TESTTYPE="${TESTTYPE}, BLOSUM" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-vt*) TESTTYPE="${TESTTYPE}, VT" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-wag*) TESTTYPE="${TESTTYPE}, WAG" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-bin) TESTTYPE="${TESTTYPE}binary data" DATA=bin INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/primates.b INUTREESOURCE=../data/primates.trees INCTREESOURCE=../data/primates.ctrees echo d > $PARAMS echo d >> $PARAMS echo d >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}default data, default model" ;; esac case "$TEST_PREF" in *-clock*) TESTTYPE="${TESTTYPE}, clock" echo z >> $PARAMS ;; esac case "$TEST_PREF" in *-rhet4*) TESTTYPE="${TESTTYPE}, rate heterogeneity (4 rates)" echo w >> $PARAMS echo c >> $PARAMS echo 4 >> $PARAMS ;; *-rhet*) TESTTYPE="${TESTTYPE}, rate heterogeneity" echo w >> $PARAMS ;; esac CHECK_PREF=check-$INFILE case "$TEST_PREF" in qp-*) TESTTYPE="${TESTTYPE}, quartet puzzling" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; lm-*) TESTTYPE="${TESTTYPE}, likelihood mapping" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo b >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; ut-*) TESTTYPE="${TESTTYPE}, user tree evaluation" cp $INFILESOURCE $INFILE cp $INUTREESOURCE $INUTREE RESULT_PREF=$INUTREE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INUTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; cons-*) TESTTYPE="${TESTTYPE}, consensus construction" cp $INFILESOURCE $INFILE cp $INCTREESOURCE $INCTREE RESULT_PREF=$INCTREE echo k >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INCTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; *) echo; echo "$TESTTYPE ($TEST_PREF)" echo UNKNOWN analysis type: test ignored exit 77 ;; esac if test $GENERATE == 1; then cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > check-${TEST_PREF} exit 0 else cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? exit $result fi tree-puzzle-5.2/tests/qp-hky-rhet-clock-nucl.test0000755000076400001440000001622410073365716015613 #! /bin/sh # # template-test # # # Part of TREE-PUZZLE 5.2 (July 2004) # # (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler # (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, # M. Vingron, and Arndt von Haeseler # (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler # # All parts of the source except where indicated are distributed under # the GNU public licence. See http://www.opensource.org for details. # # ($Id$) # fname=`echo $0 | sed 's/.*\///'` GENERATE=0 TESTTYPE="Testing: " if test 0 -ne $# then case "$1" in -g*) GENERATE=1 TESTTYPE="Generating: " ;; *) echo "Usage: $fname [-g] " echo echo " Test a TREE-PUZZLE scenario." echo " With -g no test is performed, but the " echo " template for a future test is created." echo exit 1 ;; esac fi ########################################################################## TEST_PREF=`echo $fname | sed s/\.test//` INUTREE=${TEST_PREF}.trees INCTREE=${TEST_PREF}.ctrees PARAMS=${TEST_PREF}.param # default DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees # # data type # case "$TEST_PREF" in *-nucl) TESTTYPE="${TESTTYPE}nucleotide data" DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees echo d > $PARAMS case "$TEST_PREF" in *-hky*) TESTTYPE="${TESTTYPE}, HKY" ;; *-tn*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS ;; *-gtr*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS echo m >> $PARAMS ;; *-sh*) TESTTYPE="${TESTTYPE}, SH" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-prot) TESTTYPE="${TESTTYPE}protein data" DATA=prot INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/globin.a INUTREESOURCE=../data/globin.trees INCTREESOURCE=../data/globin.ctrees echo d > $PARAMS echo d >> $PARAMS case "$TEST_PREF" in *-dayhoff*) TESTTYPE="${TESTTYPE}, Dayhoff" echo m >> $PARAMS ;; *-jtt*) TESTTYPE="${TESTTYPE}, JTT" echo m >> $PARAMS echo m >> $PARAMS ;; *-mtrev*) TESTTYPE="${TESTTYPE}, mtREV" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-blosum*) TESTTYPE="${TESTTYPE}, BLOSUM" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-vt*) TESTTYPE="${TESTTYPE}, VT" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-wag*) TESTTYPE="${TESTTYPE}, WAG" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-bin) TESTTYPE="${TESTTYPE}binary data" DATA=bin INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/primates.b INUTREESOURCE=../data/primates.trees INCTREESOURCE=../data/primates.ctrees echo d > $PARAMS echo d >> $PARAMS echo d >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}default data, default model" ;; esac case "$TEST_PREF" in *-clock*) TESTTYPE="${TESTTYPE}, clock" echo z >> $PARAMS ;; esac case "$TEST_PREF" in *-rhet4*) TESTTYPE="${TESTTYPE}, rate heterogeneity (4 rates)" echo w >> $PARAMS echo c >> $PARAMS echo 4 >> $PARAMS ;; *-rhet*) TESTTYPE="${TESTTYPE}, rate heterogeneity" echo w >> $PARAMS ;; esac CHECK_PREF=check-$INFILE case "$TEST_PREF" in qp-*) TESTTYPE="${TESTTYPE}, quartet puzzling" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; lm-*) TESTTYPE="${TESTTYPE}, likelihood mapping" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo b >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; ut-*) TESTTYPE="${TESTTYPE}, user tree evaluation" cp $INFILESOURCE $INFILE cp $INUTREESOURCE $INUTREE RESULT_PREF=$INUTREE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INUTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; cons-*) TESTTYPE="${TESTTYPE}, consensus construction" cp $INFILESOURCE $INFILE cp $INCTREESOURCE $INCTREE RESULT_PREF=$INCTREE echo k >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INCTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; *) echo; echo "$TESTTYPE ($TEST_PREF)" echo UNKNOWN analysis type: test ignored exit 77 ;; esac if test $GENERATE == 1; then cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > check-${TEST_PREF} exit 0 else cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? exit $result fi tree-puzzle-5.2/tests/ut-pure-prot.test0000755000076400001440000001622410073365716013775 #! /bin/sh # # template-test # # # Part of TREE-PUZZLE 5.2 (July 2004) # # (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler # (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, # M. Vingron, and Arndt von Haeseler # (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler # # All parts of the source except where indicated are distributed under # the GNU public licence. See http://www.opensource.org for details. # # ($Id$) # fname=`echo $0 | sed 's/.*\///'` GENERATE=0 TESTTYPE="Testing: " if test 0 -ne $# then case "$1" in -g*) GENERATE=1 TESTTYPE="Generating: " ;; *) echo "Usage: $fname [-g] " echo echo " Test a TREE-PUZZLE scenario." echo " With -g no test is performed, but the " echo " template for a future test is created." echo exit 1 ;; esac fi ########################################################################## TEST_PREF=`echo $fname | sed s/\.test//` INUTREE=${TEST_PREF}.trees INCTREE=${TEST_PREF}.ctrees PARAMS=${TEST_PREF}.param # default DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees # # data type # case "$TEST_PREF" in *-nucl) TESTTYPE="${TESTTYPE}nucleotide data" DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees echo d > $PARAMS case "$TEST_PREF" in *-hky*) TESTTYPE="${TESTTYPE}, HKY" ;; *-tn*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS ;; *-gtr*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS echo m >> $PARAMS ;; *-sh*) TESTTYPE="${TESTTYPE}, SH" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-prot) TESTTYPE="${TESTTYPE}protein data" DATA=prot INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/globin.a INUTREESOURCE=../data/globin.trees INCTREESOURCE=../data/globin.ctrees echo d > $PARAMS echo d >> $PARAMS case "$TEST_PREF" in *-dayhoff*) TESTTYPE="${TESTTYPE}, Dayhoff" echo m >> $PARAMS ;; *-jtt*) TESTTYPE="${TESTTYPE}, JTT" echo m >> $PARAMS echo m >> $PARAMS ;; *-mtrev*) TESTTYPE="${TESTTYPE}, mtREV" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-blosum*) TESTTYPE="${TESTTYPE}, BLOSUM" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-vt*) TESTTYPE="${TESTTYPE}, VT" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-wag*) TESTTYPE="${TESTTYPE}, WAG" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-bin) TESTTYPE="${TESTTYPE}binary data" DATA=bin INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/primates.b INUTREESOURCE=../data/primates.trees INCTREESOURCE=../data/primates.ctrees echo d > $PARAMS echo d >> $PARAMS echo d >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}default data, default model" ;; esac case "$TEST_PREF" in *-clock*) TESTTYPE="${TESTTYPE}, clock" echo z >> $PARAMS ;; esac case "$TEST_PREF" in *-rhet4*) TESTTYPE="${TESTTYPE}, rate heterogeneity (4 rates)" echo w >> $PARAMS echo c >> $PARAMS echo 4 >> $PARAMS ;; *-rhet*) TESTTYPE="${TESTTYPE}, rate heterogeneity" echo w >> $PARAMS ;; esac CHECK_PREF=check-$INFILE case "$TEST_PREF" in qp-*) TESTTYPE="${TESTTYPE}, quartet puzzling" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; lm-*) TESTTYPE="${TESTTYPE}, likelihood mapping" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo b >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; ut-*) TESTTYPE="${TESTTYPE}, user tree evaluation" cp $INFILESOURCE $INFILE cp $INUTREESOURCE $INUTREE RESULT_PREF=$INUTREE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INUTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; cons-*) TESTTYPE="${TESTTYPE}, consensus construction" cp $INFILESOURCE $INFILE cp $INCTREESOURCE $INCTREE RESULT_PREF=$INCTREE echo k >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INCTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; *) echo; echo "$TESTTYPE ($TEST_PREF)" echo UNKNOWN analysis type: test ignored exit 77 ;; esac if test $GENERATE == 1; then cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > check-${TEST_PREF} exit 0 else cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? exit $result fi tree-puzzle-5.2/tests/check-cons-pure-prot0000644000076400001440000001442110073365742014375 TREE-PUZZLE Input file name: cons-pure-prot.prot User tree file name: cons-pure-prot.ctrees Type of analysis: consensus construction Parameter estimation: approximate (faster) Parameter estimation uses: 1st user tree (for substitution process and rate variation) Standard errors (S.E.) are obtained by the curvature method. The upper and lower bounds of an approximate 95% confidence interval for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. SEQUENCE ALIGNMENT Input data: 7 sequences with 128 amino acid sites Number of constant sites: 7 (= 5.5% of all sites) Number of site patterns: 125 Number of constant site patterns: 5 (= 4.0% of all site patterns) SUBSTITUTION PROCESS Model of substitution: Dayhoff (Dayhoff et al. 1978) Amino acid frequencies (estimated from data set): pi(A) = 12.2% pi(R) = 2.3% pi(N) = 3.0% pi(D) = 4.9% pi(C) = 0.7% pi(Q) = 2.3% pi(E) = 5.4% pi(G) = 6.0% pi(H) = 5.8% pi(I) = 2.7% pi(L) = 12.5% pi(K) = 9.3% pi(M) = 1.3% pi(F) = 4.9% pi(P) = 2.6% pi(S) = 6.7% pi(T) = 4.5% pi(W) = 1.3% pi(Y) = 2.2% pi(V) = 9.4% AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) gaps wildcards sum % sequence HBB_HUMAN 0 0 0 0.00% HBB_HORSE 0 0 0 0.00% HBA_HUMAN 0 0 0 0.00% HBA_HORSE 0 0 0 0.00% MYG_PHYCA 0 0 0 0.00% GLB5_PETMA 0 0 0 0.00% LGB2_LUPLU 0 0 0 0.00% ------------------------------------------------------- Sum 0 0 0 0.00% The table above shows the amount of gaps ('-') and other 'wildcard' characters ('X', '?', etc.) and their percentage of the 128 columns in the alignment. Sequences with more than 50% ambiguous characters are marked with a '!' and should be checked, whether they have sufficient overlap to other sequences. Sequences with 100% ambiguous characters do not hold any phylogenetic information and had to be discarded from the analysis. SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) 5% chi-square test p-value HBB_HUMAN passed 92.31% HBB_HORSE passed 79.58% HBA_HUMAN passed 93.09% HBA_HORSE passed 81.20% MYG_PHYCA passed 33.23% GLB5_PETMA passed 19.11% LGB2_LUPLU passed 41.67% The chi-square tests compares the amino acid composition of each sequence to the frequency distribution assumed in the maximum likelihood model. WARNING: Result of chi-square test may not be valid because of small maximum likelihood frequencies and short sequence length! IDENTICAL SEQUENCES The sequences in each of the following groups are all identical. To speed up computation please remove all but one of each group from the data set. All sequences are unique. MAXIMUM LIKELIHOOD DISTANCES Maximum likelihood distances are computed using the selected model of substitution and rate heterogeneity. 7 HBB_HUMAN 0.00000 0.17425 0.96068 0.99267 2.12932 1.77231 2.78644 HBB_HORSE 0.17425 0.00000 1.01062 1.02118 2.09456 1.78465 2.86187 HBA_HUMAN 0.96068 1.01062 0.00000 0.12147 1.93540 1.30123 2.54730 HBA_HORSE 0.99267 1.02118 0.12147 0.00000 2.00515 1.39193 2.51172 MYG_PHYCA 2.12932 2.09456 1.93540 2.00515 0.00000 2.12347 2.79386 GLB5_PETMA 1.77231 1.78465 1.30123 1.39193 2.12347 0.00000 2.18272 LGB2_LUPLU 2.78644 2.86187 2.54730 2.51172 2.79386 2.18272 0.00000 Average distance (over all possible pairs of sequences): 1.73823 minimum : 0.12147, maximum : 2.86187 variance : 0.65214, std.dev. : 0.80755 RATE HETEROGENEITY Model of rate heterogeneity: uniform rate TREE SEARCH 100 tree topologies were specified by the user. CONSENSUS TREE Support for the internal branches of the unrooted consensus tree topology is shown in percent. This consensus tree is not completely resolved! :---HBA_HUMAN :100: : :---HBA_HORSE :100: : : :---MYG_PHYCA : : : : :100:---GLB5_PETMA : : : :---LGB2_LUPLU : :-----------HBB_HORSE : :-----------HBB_HUMAN Consensus tree (in CLUSTAL W notation): (HBB_HUMAN,((HBA_HUMAN,HBA_HORSE)100,(MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)100)100, HBB_HORSE); BIPARTITIONS The following bipartitions occured at least once in the specified set of 100 usertrees tree topologies. Bipartitions included in the consensus tree: (bipartition with sequences in input order : number of times seen) **..*** : 100 ****... : 100 **..... : 100 Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen) ****..* : 40 Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen) *****.. : 37 ****.*. : 23 MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :-3 HBA_HUMAN :----8 : :-4 HBA_HORSE :------10 : : :-------------5 MYG_PHYCA : :-----9 : :-------6 GLB5_PETMA : : : :-----------------7 LGB2_LUPLU : :--2 HBB_HORSE : :-1 HBB_HUMAN branch length S.E. branch length S.E. HBB_HUMAN 1 0.04834 0.03148 8 0.28040 0.08746 HBB_HORSE 2 0.12685 0.03876 9 0.40362 0.12823 HBA_HUMAN 3 0.02653 0.02208 10 0.60481 0.11281 HBA_HORSE 4 0.09440 0.03145 MYG_PHYCA 5 1.33099 0.21112 GLB5_PETMA 6 0.70102 0.14139 10 iterations until convergence LGB2_LUPLU 7 1.76831 0.28198 log L: -1699.50 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): (HBB_HUMAN:0.04834,((HBA_HUMAN:0.02653,HBA_HORSE:0.09440)100:0.28040, (MYG_PHYCA:1.33099,GLB5_PETMA:0.70102,LGB2_LUPLU:1.76831)100:0.40362) 100:0.60481,HBB_HORSE:0.12685); TIME STAMP tree-puzzle-5.2/tests/qp-hky-rhet-nucl.test0000755000076400001440000001622410073365716014522 #! /bin/sh # # template-test # # # Part of TREE-PUZZLE 5.2 (July 2004) # # (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler # (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, # M. Vingron, and Arndt von Haeseler # (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler # # All parts of the source except where indicated are distributed under # the GNU public licence. See http://www.opensource.org for details. # # ($Id$) # fname=`echo $0 | sed 's/.*\///'` GENERATE=0 TESTTYPE="Testing: " if test 0 -ne $# then case "$1" in -g*) GENERATE=1 TESTTYPE="Generating: " ;; *) echo "Usage: $fname [-g] " echo echo " Test a TREE-PUZZLE scenario." echo " With -g no test is performed, but the " echo " template for a future test is created." echo exit 1 ;; esac fi ########################################################################## TEST_PREF=`echo $fname | sed s/\.test//` INUTREE=${TEST_PREF}.trees INCTREE=${TEST_PREF}.ctrees PARAMS=${TEST_PREF}.param # default DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees # # data type # case "$TEST_PREF" in *-nucl) TESTTYPE="${TESTTYPE}nucleotide data" DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees echo d > $PARAMS case "$TEST_PREF" in *-hky*) TESTTYPE="${TESTTYPE}, HKY" ;; *-tn*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS ;; *-gtr*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS echo m >> $PARAMS ;; *-sh*) TESTTYPE="${TESTTYPE}, SH" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-prot) TESTTYPE="${TESTTYPE}protein data" DATA=prot INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/globin.a INUTREESOURCE=../data/globin.trees INCTREESOURCE=../data/globin.ctrees echo d > $PARAMS echo d >> $PARAMS case "$TEST_PREF" in *-dayhoff*) TESTTYPE="${TESTTYPE}, Dayhoff" echo m >> $PARAMS ;; *-jtt*) TESTTYPE="${TESTTYPE}, JTT" echo m >> $PARAMS echo m >> $PARAMS ;; *-mtrev*) TESTTYPE="${TESTTYPE}, mtREV" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-blosum*) TESTTYPE="${TESTTYPE}, BLOSUM" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-vt*) TESTTYPE="${TESTTYPE}, VT" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-wag*) TESTTYPE="${TESTTYPE}, WAG" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-bin) TESTTYPE="${TESTTYPE}binary data" DATA=bin INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/primates.b INUTREESOURCE=../data/primates.trees INCTREESOURCE=../data/primates.ctrees echo d > $PARAMS echo d >> $PARAMS echo d >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}default data, default model" ;; esac case "$TEST_PREF" in *-clock*) TESTTYPE="${TESTTYPE}, clock" echo z >> $PARAMS ;; esac case "$TEST_PREF" in *-rhet4*) TESTTYPE="${TESTTYPE}, rate heterogeneity (4 rates)" echo w >> $PARAMS echo c >> $PARAMS echo 4 >> $PARAMS ;; *-rhet*) TESTTYPE="${TESTTYPE}, rate heterogeneity" echo w >> $PARAMS ;; esac CHECK_PREF=check-$INFILE case "$TEST_PREF" in qp-*) TESTTYPE="${TESTTYPE}, quartet puzzling" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; lm-*) TESTTYPE="${TESTTYPE}, likelihood mapping" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo b >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; ut-*) TESTTYPE="${TESTTYPE}, user tree evaluation" cp $INFILESOURCE $INFILE cp $INUTREESOURCE $INUTREE RESULT_PREF=$INUTREE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INUTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; cons-*) TESTTYPE="${TESTTYPE}, consensus construction" cp $INFILESOURCE $INFILE cp $INCTREESOURCE $INCTREE RESULT_PREF=$INCTREE echo k >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INCTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; *) echo; echo "$TESTTYPE ($TEST_PREF)" echo UNKNOWN analysis type: test ignored exit 77 ;; esac if test $GENERATE == 1; then cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > check-${TEST_PREF} exit 0 else cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? exit $result fi tree-puzzle-5.2/tests/check-qp-pure-bin0000644000076400001440000001542510073365716013645 TREE-PUZZLE Input file name: qp-pure-bin.bin Type of analysis: tree reconstruction Parameter estimation: approximate (faster) Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) Standard errors (S.E.) are obtained by the curvature method. The upper and lower bounds of an approximate 95% confidence interval for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. SEQUENCE ALIGNMENT Input data: 5 sequences with 895 binary state sites Number of constant sites: 825 (= 92.2% of all sites) Number of site patterns: 16 Number of constant site patterns: 2 (= 12.5% of all site patterns) SUBSTITUTION PROCESS Model of substitution: Two-state model (Felsenstein 1981) Binary state frequencies (estimated from data set): pi(0) = 41.8% pi(1) = 58.2% AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) gaps wildcards sum % sequence Gibbon 0 0 0 0.00% Human 0 0 0 0.00% Chimpanzee 0 0 0 0.00% Gorilla 0 0 0 0.00% Orangutan 0 0 0 0.00% ------------------------------------------------------- Sum 0 0 0 0.00% The table above shows the amount of gaps ('-') and other 'wildcard' characters ('X', '?', etc.) and their percentage of the 895 columns in the alignment. Sequences with more than 50% ambiguous characters are marked with a '!' and should be checked, whether they have sufficient overlap to other sequences. Sequences with 100% ambiguous characters do not hold any phylogenetic information and had to be discarded from the analysis. SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) 5% chi-square test p-value Gibbon passed 41.61% Human passed 73.47% Chimpanzee passed 68.43% Gorilla passed 94.60% Orangutan passed 100.00% The chi-square tests compares the binary state composition of each sequence to the frequency distribution assumed in the maximum likelihood model. IDENTICAL SEQUENCES The sequences in each of the following groups are all identical. To speed up computation please remove all but one of each group from the data set. All sequences are unique. MAXIMUM LIKELIHOOD DISTANCES Maximum likelihood distances are computed using the selected model of substitution and rate heterogeneity. 5 Gibbon 0.00000 0.05300 0.05176 0.05295 0.06171 Human 0.05300 0.00000 0.00563 0.00903 0.04081 Chimpanzee 0.05176 0.00563 0.00000 0.01018 0.03960 Gorilla 0.05295 0.00903 0.01018 0.00000 0.03835 Orangutan 0.06171 0.04081 0.03960 0.03835 0.00000 Average distance (over all possible pairs of sequences): 0.03630 minimum : 0.00563, maximum : 0.06171 variance : 0.00043, std.dev. : 0.02066 RATE HETEROGENEITY Model of rate heterogeneity: uniform rate QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) name | resolved | partly resolved | unresolved | sum -------------------------------------------------------------------------- Gibbon 4 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 4 Human 4 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 4 Chimpanzee 4 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 4 Gorilla 4 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 4 Orangutan 4 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 4 -------------------------------------------------------------------------- #quartets : 5 [100.00%] 0 [ 0.00%] 0 [ 0.00%] 5 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage relative to the number of times the sequence occurs in the list of quartets (i.e. 4 quartets out of 5 in total). In fully resolved quartet one single topology is supported, while for partially resolved quartets two and for completely unresolved quartets none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. Note: Because 4 sequences are involved in one quartet numbers add up to a four-fold of the existing quartets. Hint: The overall numbers in the last row give information about the phylogenetic content of the dataset. The higher the percentage of partially and unresolved quartets, the lower the content of phylogenetic information. This can be visualized in more detail by likelihood mapping analysis. TREE SEARCH Quartet puzzling is used to choose from the possible tree topologies and to simultaneously infer support values for internal branches. Number of puzzling steps: 1000 Analysed quartets: 5 Fully resolved quartets: 5 (= 100.0%) Partly resolved quartets: 0 (= 0.0%) Unresolved quartets: 0 (= 0.0%) Quartet trees are based on exact maximum likelihood values using the selected model of substitution and rate heterogeneity. QUARTET PUZZLING TREE Support for the internal branches of the unrooted quartet puzzling tree topology is shown in percent. This quartet puzzling tree is completely resolved. :---Human :100: :100: :---Chimpanzee : : : :-------Gorilla : :-----------Orangutan : :-----------Gibbon Quartet puzzling tree (in CLUSTAL W notation): (Gibbon,((Human,Chimpanzee)100,Gorilla)100,Orangutan); BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) *..** : 1000 *...* : 1000 Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen) None (all bipartitions are included) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :-2 Human :--6 : :-3 Chimpanzee :---7 : :-4 Gorilla : :---5 Orangutan : :----1 Gibbon branch length S.E. branch length S.E. Gibbon 1 0.03803 0.00691 6 0.00339 0.00199 Human 2 0.00240 0.00170 7 0.01106 0.00384 Chimpanzee 3 0.00323 0.00196 Gorilla 4 0.00353 0.00206 5 iterations until convergence Orangutan 5 0.02357 0.00543 log L: -968.78 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Gibbon:0.03803,((Human:0.00240,Chimpanzee:0.00323)100:0.00339,Gorilla:0.00353) 100:0.01106,Orangutan:0.02357); TIME STAMP tree-puzzle-5.2/tests/qp-jtt-rhet-prot.test0000755000076400001440000001622410073365716014553 #! /bin/sh # # template-test # # # Part of TREE-PUZZLE 5.2 (July 2004) # # (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler # (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, # M. Vingron, and Arndt von Haeseler # (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler # # All parts of the source except where indicated are distributed under # the GNU public licence. See http://www.opensource.org for details. # # ($Id$) # fname=`echo $0 | sed 's/.*\///'` GENERATE=0 TESTTYPE="Testing: " if test 0 -ne $# then case "$1" in -g*) GENERATE=1 TESTTYPE="Generating: " ;; *) echo "Usage: $fname [-g] " echo echo " Test a TREE-PUZZLE scenario." echo " With -g no test is performed, but the " echo " template for a future test is created." echo exit 1 ;; esac fi ########################################################################## TEST_PREF=`echo $fname | sed s/\.test//` INUTREE=${TEST_PREF}.trees INCTREE=${TEST_PREF}.ctrees PARAMS=${TEST_PREF}.param # default DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees # # data type # case "$TEST_PREF" in *-nucl) TESTTYPE="${TESTTYPE}nucleotide data" DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees echo d > $PARAMS case "$TEST_PREF" in *-hky*) TESTTYPE="${TESTTYPE}, HKY" ;; *-tn*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS ;; *-gtr*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS echo m >> $PARAMS ;; *-sh*) TESTTYPE="${TESTTYPE}, SH" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-prot) TESTTYPE="${TESTTYPE}protein data" DATA=prot INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/globin.a INUTREESOURCE=../data/globin.trees INCTREESOURCE=../data/globin.ctrees echo d > $PARAMS echo d >> $PARAMS case "$TEST_PREF" in *-dayhoff*) TESTTYPE="${TESTTYPE}, Dayhoff" echo m >> $PARAMS ;; *-jtt*) TESTTYPE="${TESTTYPE}, JTT" echo m >> $PARAMS echo m >> $PARAMS ;; *-mtrev*) TESTTYPE="${TESTTYPE}, mtREV" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-blosum*) TESTTYPE="${TESTTYPE}, BLOSUM" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-vt*) TESTTYPE="${TESTTYPE}, VT" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-wag*) TESTTYPE="${TESTTYPE}, WAG" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-bin) TESTTYPE="${TESTTYPE}binary data" DATA=bin INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/primates.b INUTREESOURCE=../data/primates.trees INCTREESOURCE=../data/primates.ctrees echo d > $PARAMS echo d >> $PARAMS echo d >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}default data, default model" ;; esac case "$TEST_PREF" in *-clock*) TESTTYPE="${TESTTYPE}, clock" echo z >> $PARAMS ;; esac case "$TEST_PREF" in *-rhet4*) TESTTYPE="${TESTTYPE}, rate heterogeneity (4 rates)" echo w >> $PARAMS echo c >> $PARAMS echo 4 >> $PARAMS ;; *-rhet*) TESTTYPE="${TESTTYPE}, rate heterogeneity" echo w >> $PARAMS ;; esac CHECK_PREF=check-$INFILE case "$TEST_PREF" in qp-*) TESTTYPE="${TESTTYPE}, quartet puzzling" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; lm-*) TESTTYPE="${TESTTYPE}, likelihood mapping" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo b >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; ut-*) TESTTYPE="${TESTTYPE}, user tree evaluation" cp $INFILESOURCE $INFILE cp $INUTREESOURCE $INUTREE RESULT_PREF=$INUTREE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INUTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; cons-*) TESTTYPE="${TESTTYPE}, consensus construction" cp $INFILESOURCE $INFILE cp $INCTREESOURCE $INCTREE RESULT_PREF=$INCTREE echo k >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INCTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; *) echo; echo "$TESTTYPE ($TEST_PREF)" echo UNKNOWN analysis type: test ignored exit 77 ;; esac if test $GENERATE == 1; then cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > check-${TEST_PREF} exit 0 else cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? exit $result fi tree-puzzle-5.2/tests/check-qp-clock0000644000076400001440000002702210073365723013211 TREE-PUZZLE Input file name: qp-clock.nucl Type of analysis: tree reconstruction Parameter estimation: approximate (faster) Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) Standard errors (S.E.) are obtained by the curvature method. The upper and lower bounds of an approximate 95% confidence interval for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. SEQUENCE ALIGNMENT Input data: 8 sequences with 116 nucleotide sites Number of constant sites: 66 (= 56.9% of all sites) Number of site patterns: 54 Number of constant site patterns: 4 (= 7.4% of all site patterns) SUBSTITUTION PROCESS Model of substitution: HKY (Hasegawa et al. 1985) Transition/transversion parameter (estimated from data set): 1.51 (S.E. 0.28) Rate matrix R (parameters restricted to selected model): A-C rate: 1.00000 A-G rate: 2.98614 A-T rate: 1.00000 C-G rate: 1.00000 C-T rate: 2.98614 G-T rate: 1.00000 Nucleotide frequencies (estimated from data set): pi(A) = 26.6% pi(C) = 30.6% pi(G) = 12.0% pi(T) = 30.7% Expected transition/transversion ratio: 1.60 Expected pyrimidine transition/purine transition ratio: 2.95 AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) gaps wildcards sum % sequence Thylacinus 0 0 0 0.00% Sarcophilu 0 0 0 0.00% Dasyurus 0 1 1 0.86% Echymipera 0 0 0 0.00% Trichosuru 0 0 0 0.00% Phalanger 0 0 0 0.00% Philander 0 0 0 0.00% Bos 0 0 0 0.00% ------------------------------------------------------- Sum 0 1 1 0.11% The table above shows the amount of gaps ('-') and other 'wildcard' characters ('X', '?', etc.) and their percentage of the 116 columns in the alignment. Sequences with more than 50% ambiguous characters are marked with a '!' and should be checked, whether they have sufficient overlap to other sequences. Sequences with 100% ambiguous characters do not hold any phylogenetic information and had to be discarded from the analysis. SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) 5% chi-square test p-value Thylacinus passed 90.89% Sarcophilu passed 93.32% Dasyurus passed 98.01% Echymipera passed 92.83% Trichosuru passed 90.41% Phalanger passed 86.09% Philander passed 66.19% Bos passed 60.02% The chi-square tests compares the nucleotide composition of each sequence to the frequency distribution assumed in the maximum likelihood model. IDENTICAL SEQUENCES The sequences in each of the following groups are all identical. To speed up computation please remove all but one of each group from the data set. All sequences are unique. MAXIMUM LIKELIHOOD DISTANCES Maximum likelihood distances are computed using the selected model of substitution and rate heterogeneity. 8 Thylacinus 0.00000 0.25562 0.22032 0.24509 0.26007 0.24938 0.22246 0.23734 Sarcophilu 0.25562 0.00000 0.13169 0.26969 0.28414 0.32680 0.26008 0.29786 Dasyurus 0.22032 0.13169 0.00000 0.20032 0.24821 0.25234 0.17801 0.23883 Echymipera 0.24509 0.26969 0.20032 0.00000 0.29531 0.33871 0.23041 0.27215 Trichosuru 0.26007 0.28414 0.24821 0.29531 0.00000 0.21136 0.28562 0.27148 Phalanger 0.24938 0.32680 0.25234 0.33871 0.21136 0.00000 0.29036 0.33042 Philander 0.22246 0.26008 0.17801 0.23041 0.28562 0.29036 0.00000 0.22452 Bos 0.23734 0.29786 0.23883 0.27215 0.27148 0.33042 0.22452 0.00000 Average distance (over all possible pairs of sequences): 0.25459 minimum : 0.13169, maximum : 0.33871 variance : 0.00207, std.dev. : 0.04544 RATE HETEROGENEITY Model of rate heterogeneity: uniform rate QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) name | resolved | partly resolved | unresolved | sum -------------------------------------------------------------------------- Thylacinus 22 [ 62.86%] 4 [ 11.43%] 9 [ 25.71%] 35 Sarcophilu 27 [ 77.14%] 1 [ 2.86%] 7 [ 20.00%] 35 Dasyurus 27 [ 77.14%] 4 [ 11.43%] 4 [ 11.43%] 35 Echymipera 20 [ 57.14%] 4 [ 11.43%] 11 [ 31.43%] 35 Trichosuru 27 [ 77.14%] 2 [ 5.71%] 6 [ 17.14%] 35 Phalanger 28 [ 80.00%] 3 [ 8.57%] 4 [ 11.43%] 35 Philander 25 [ 71.43%] 6 [ 17.14%] 4 [ 11.43%] 35 Bos 20 [ 57.14%] 4 [ 11.43%] 11 [ 31.43%] 35 -------------------------------------------------------------------------- #quartets : 49 [ 70.00%] 7 [ 10.00%] 14 [ 20.00%] 70 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage relative to the number of times the sequence occurs in the list of quartets (i.e. 35 quartets out of 70 in total). In fully resolved quartet one single topology is supported, while for partially resolved quartets two and for completely unresolved quartets none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. Note: Because 4 sequences are involved in one quartet numbers add up to a four-fold of the existing quartets. Hint: The overall numbers in the last row give information about the phylogenetic content of the dataset. The higher the percentage of partially and unresolved quartets, the lower the content of phylogenetic information. This can be visualized in more detail by likelihood mapping analysis. TREE SEARCH Quartet puzzling is used to choose from the possible tree topologies and to simultaneously infer support values for internal branches. Number of puzzling steps: 1000 Analysed quartets: 70 Fully resolved quartets: 49 (= 70.0%) Partly resolved quartets: 7 (= 10.0%) Unresolved quartets: 14 (= 20.0%) Quartet trees are based on approximate maximum likelihood values using the selected model of substitution and rate heterogeneity. QUARTET PUZZLING TREE Support for the internal branches of the unrooted quartet puzzling tree topology is shown in percent. This quartet puzzling tree is not completely resolved! :---Trichosuru :-----97: : :---Phalanger : : :---Sarcophilu : :-98: : : :---Dasyurus : : :-71: :---Philander : :-65: : : :---Bos : : : :-------Echymipera : :-----------Thylacinus Quartet puzzling tree (in CLUSTAL W notation): (Thylacinus,(Trichosuru,Phalanger)97,((Sarcophilu,Dasyurus)98, (Philander,Bos)65,Echymipera)71); BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) *..***** : 981 ****..** : 971 *...**.. : 713 ******.. : 649 Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen) *...**** : 426 Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen) ***.**.. : 347 ***.**.* : 150 *...**.* : 131 *..***.. : 87 *..*..** : 81 *.....** : 72 ****..*. : 55 ***.***. : 37 ****.... : 36 *..***.* : 36 ***..... : 31 *.....*. : 28 *...***. : 27 *......* : 27 *....*.. : 26 *..*.... : 21 **..**** : 16 ***...** : 14 *..*..*. : 13 *..****. : 12 (6 other less frequent bipartitions not shown) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :---------5 Trichosuru :------9 : :----------6 Phalanger : : :-----------2 Sarcophilu : :-------10 : : :-3 Dasyurus :-----12 : : :--------7 Philander : :----11 : : :-----------8 Bos : : : :------------4 Echymipera : :---------1 Thylacinus branch length S.E. branch length S.E. Thylacinus 1 0.11024 0.03812 9 0.05953 0.03382 Sarcophilu 2 0.13180 0.03734 10 0.08585 0.03452 Dasyurus 3 0.00572 0.01273 11 0.04220 0.02513 Echymipera 4 0.13997 0.04108 12 0.05457 0.02998 Trichosuru 5 0.10654 0.03770 Phalanger 6 0.12258 0.04064 Philander 7 0.08995 0.03428 8 iterations until convergence Bos 8 0.13479 0.04095 log L: -603.37 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Thylacinus:0.11024,(Trichosuru:0.10654,Phalanger:0.12258)97:0.05953, ((Sarcophilu:0.13180,Dasyurus:0.00572)98:0.08585,(Philander:0.08995, Bos:0.13479)65:0.04220,Echymipera:0.13997)71:0.05457); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF CONSENSUS TREE (WITH CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. Root located at branch: 1 "Thylacinus" (automatic search) If the automatic search misplaces the root please rerun the analysis (rename "outtree" to "intree") and select location of root manually! :---------5 Trichosuru :-----9 : :---------6 Phalanger : : :-----2 Sarcophilu : :------10 : : :-----3 Dasyurus :--12 : : :--------7 Philander : :---11 : : :--------8 Bos : : : :-----------4 Echymipera : :------------1 Thylacinus Tree drawn as unrooted tree for better comparison with non-clock tree! branch length nc/c branch length nc/c (= non-clock/clock) Thylacinus 1 0.14706 0.750 9 0.04504 1.322 Sarcophilu 2 0.06189 2.130 10 0.06663 1.288 Dasyurus 3 0.06189 0.092 11 0.03304 1.277 Echymipera 4 0.12852 1.089 12 0.01851 2.948 Trichosuru 5 0.10199 1.045 Phalanger 6 0.10199 1.202 Philander 7 0.09549 0.942 6 iterations until convergence Bos 8 0.09549 1.412 log L: -610.75 height S.E. of node common to branches 0.10199 0.01922 9 5 6 0.06189 0.01495 10 2 3 0.09549 0.01498 11 7 8 0.12852 0.01108 12 10 11 4 0.14704 0.01235 1 9 12 0.14705 0.02366 of root at branch 1 Rooted consensus tree with clocklike maximum likelihood branch lengths (in CLUSTAL W notation): (Thylacinus:0.14705,((Trichosuru:0.10199,Phalanger:0.10199)97:0.04504 ,((Sarcophilu:0.06189,Dasyurus:0.06189)98:0.06663,(Philander:0.09549, Bos:0.09549)65:0.03304,Echymipera:0.12852)71:0.01851):0.00001); MOLECULAR CLOCK LIKELIHOOD RATIO TEST log L without clock: -603.37 (independent branch parameters: 12) log L with clock: -610.75 (independent branch parameters: 6) Likelihood ratio test statistic delta: 14.77 Degress of freedom of chi-square distribution: 6 Critical significance level: 2.22% The simpler (clocklike) tree is rejected on a significance level of 5%. The log-likelihood of the more complex (no clock) tree is significantly increased. Please take care that the correct root is used! TIME STAMP tree-puzzle-5.2/tests/qp-jtt-prot.test0000755000076400001440000001622410073365716013613 #! /bin/sh # # template-test # # # Part of TREE-PUZZLE 5.2 (July 2004) # # (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler # (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, # M. Vingron, and Arndt von Haeseler # (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler # # All parts of the source except where indicated are distributed under # the GNU public licence. See http://www.opensource.org for details. # # ($Id$) # fname=`echo $0 | sed 's/.*\///'` GENERATE=0 TESTTYPE="Testing: " if test 0 -ne $# then case "$1" in -g*) GENERATE=1 TESTTYPE="Generating: " ;; *) echo "Usage: $fname [-g] " echo echo " Test a TREE-PUZZLE scenario." echo " With -g no test is performed, but the " echo " template for a future test is created." echo exit 1 ;; esac fi ########################################################################## TEST_PREF=`echo $fname | sed s/\.test//` INUTREE=${TEST_PREF}.trees INCTREE=${TEST_PREF}.ctrees PARAMS=${TEST_PREF}.param # default DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees # # data type # case "$TEST_PREF" in *-nucl) TESTTYPE="${TESTTYPE}nucleotide data" DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees echo d > $PARAMS case "$TEST_PREF" in *-hky*) TESTTYPE="${TESTTYPE}, HKY" ;; *-tn*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS ;; *-gtr*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS echo m >> $PARAMS ;; *-sh*) TESTTYPE="${TESTTYPE}, SH" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-prot) TESTTYPE="${TESTTYPE}protein data" DATA=prot INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/globin.a INUTREESOURCE=../data/globin.trees INCTREESOURCE=../data/globin.ctrees echo d > $PARAMS echo d >> $PARAMS case "$TEST_PREF" in *-dayhoff*) TESTTYPE="${TESTTYPE}, Dayhoff" echo m >> $PARAMS ;; *-jtt*) TESTTYPE="${TESTTYPE}, JTT" echo m >> $PARAMS echo m >> $PARAMS ;; *-mtrev*) TESTTYPE="${TESTTYPE}, mtREV" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-blosum*) TESTTYPE="${TESTTYPE}, BLOSUM" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-vt*) TESTTYPE="${TESTTYPE}, VT" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-wag*) TESTTYPE="${TESTTYPE}, WAG" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-bin) TESTTYPE="${TESTTYPE}binary data" DATA=bin INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/primates.b INUTREESOURCE=../data/primates.trees INCTREESOURCE=../data/primates.ctrees echo d > $PARAMS echo d >> $PARAMS echo d >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}default data, default model" ;; esac case "$TEST_PREF" in *-clock*) TESTTYPE="${TESTTYPE}, clock" echo z >> $PARAMS ;; esac case "$TEST_PREF" in *-rhet4*) TESTTYPE="${TESTTYPE}, rate heterogeneity (4 rates)" echo w >> $PARAMS echo c >> $PARAMS echo 4 >> $PARAMS ;; *-rhet*) TESTTYPE="${TESTTYPE}, rate heterogeneity" echo w >> $PARAMS ;; esac CHECK_PREF=check-$INFILE case "$TEST_PREF" in qp-*) TESTTYPE="${TESTTYPE}, quartet puzzling" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; lm-*) TESTTYPE="${TESTTYPE}, likelihood mapping" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo b >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; ut-*) TESTTYPE="${TESTTYPE}, user tree evaluation" cp $INFILESOURCE $INFILE cp $INUTREESOURCE $INUTREE RESULT_PREF=$INUTREE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INUTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; cons-*) TESTTYPE="${TESTTYPE}, consensus construction" cp $INFILESOURCE $INFILE cp $INCTREESOURCE $INCTREE RESULT_PREF=$INCTREE echo k >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INCTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; *) echo; echo "$TESTTYPE ($TEST_PREF)" echo UNKNOWN analysis type: test ignored exit 77 ;; esac if test $GENERATE == 1; then cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > check-${TEST_PREF} exit 0 else cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? exit $result fi tree-puzzle-5.2/tests/check-qp-wag-prot0000644000076400001440000002060310073365723013654 TREE-PUZZLE Input file name: qp-wag-prot.prot Type of analysis: tree reconstruction Parameter estimation: approximate (faster) Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) Standard errors (S.E.) are obtained by the curvature method. The upper and lower bounds of an approximate 95% confidence interval for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. SEQUENCE ALIGNMENT Input data: 7 sequences with 128 amino acid sites Number of constant sites: 7 (= 5.5% of all sites) Number of site patterns: 125 Number of constant site patterns: 5 (= 4.0% of all site patterns) SUBSTITUTION PROCESS Model of substitution: WAG (Whelan-Goldman 2000) Amino acid frequencies (estimated from data set): pi(A) = 12.2% pi(R) = 2.3% pi(N) = 3.0% pi(D) = 4.9% pi(C) = 0.7% pi(Q) = 2.3% pi(E) = 5.4% pi(G) = 6.0% pi(H) = 5.8% pi(I) = 2.7% pi(L) = 12.5% pi(K) = 9.3% pi(M) = 1.3% pi(F) = 4.9% pi(P) = 2.6% pi(S) = 6.7% pi(T) = 4.5% pi(W) = 1.3% pi(Y) = 2.2% pi(V) = 9.4% AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) gaps wildcards sum % sequence HBB_HUMAN 0 0 0 0.00% HBB_HORSE 0 0 0 0.00% HBA_HUMAN 0 0 0 0.00% HBA_HORSE 0 0 0 0.00% MYG_PHYCA 0 0 0 0.00% GLB5_PETMA 0 0 0 0.00% LGB2_LUPLU 0 0 0 0.00% ------------------------------------------------------- Sum 0 0 0 0.00% The table above shows the amount of gaps ('-') and other 'wildcard' characters ('X', '?', etc.) and their percentage of the 128 columns in the alignment. Sequences with more than 50% ambiguous characters are marked with a '!' and should be checked, whether they have sufficient overlap to other sequences. Sequences with 100% ambiguous characters do not hold any phylogenetic information and had to be discarded from the analysis. SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) 5% chi-square test p-value HBB_HUMAN passed 92.31% HBB_HORSE passed 79.58% HBA_HUMAN passed 93.09% HBA_HORSE passed 81.20% MYG_PHYCA passed 33.23% GLB5_PETMA passed 19.11% LGB2_LUPLU passed 41.67% The chi-square tests compares the amino acid composition of each sequence to the frequency distribution assumed in the maximum likelihood model. WARNING: Result of chi-square test may not be valid because of small maximum likelihood frequencies and short sequence length! IDENTICAL SEQUENCES The sequences in each of the following groups are all identical. To speed up computation please remove all but one of each group from the data set. All sequences are unique. MAXIMUM LIKELIHOOD DISTANCES Maximum likelihood distances are computed using the selected model of substitution and rate heterogeneity. 7 HBB_HUMAN 0.00000 0.16900 0.89717 0.92939 1.84037 1.59398 2.23038 HBB_HORSE 0.16900 0.00000 0.92202 0.93317 1.80081 1.60452 2.27765 HBA_HUMAN 0.89717 0.92202 0.00000 0.12400 1.71106 1.17087 2.28564 HBA_HORSE 0.92939 0.93317 0.12400 0.00000 1.77692 1.23977 2.22372 MYG_PHYCA 1.84037 1.80081 1.71106 1.77692 0.00000 1.72932 2.25004 GLB5_PETMA 1.59398 1.60452 1.17087 1.23977 1.72932 0.00000 1.91159 LGB2_LUPLU 2.23038 2.27765 2.28564 2.22372 2.25004 1.91159 0.00000 Average distance (over all possible pairs of sequences): 1.50578 minimum : 0.12400, maximum : 2.28564 variance : 0.42979, std.dev. : 0.65558 RATE HETEROGENEITY Model of rate heterogeneity: uniform rate QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) name | resolved | partly resolved | unresolved | sum -------------------------------------------------------------------------- HBB_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 HBB_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 HBA_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 HBA_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 MYG_PHYCA 16 [ 80.00%] 0 [ 0.00%] 4 [ 20.00%] 20 GLB5_PETMA 16 [ 80.00%] 0 [ 0.00%] 4 [ 20.00%] 20 LGB2_LUPLU 16 [ 80.00%] 0 [ 0.00%] 4 [ 20.00%] 20 -------------------------------------------------------------------------- #quartets : 31 [ 88.57%] 0 [ 0.00%] 4 [ 11.43%] 35 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage relative to the number of times the sequence occurs in the list of quartets (i.e. 20 quartets out of 35 in total). In fully resolved quartet one single topology is supported, while for partially resolved quartets two and for completely unresolved quartets none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. Note: Because 4 sequences are involved in one quartet numbers add up to a four-fold of the existing quartets. Hint: The overall numbers in the last row give information about the phylogenetic content of the dataset. The higher the percentage of partially and unresolved quartets, the lower the content of phylogenetic information. This can be visualized in more detail by likelihood mapping analysis. TREE SEARCH Quartet puzzling is used to choose from the possible tree topologies and to simultaneously infer support values for internal branches. Number of puzzling steps: 1000 Analysed quartets: 35 Fully resolved quartets: 31 (= 88.6%) Partly resolved quartets: 0 (= 0.0%) Unresolved quartets: 4 (= 11.4%) Quartet trees are based on approximate maximum likelihood values using the selected model of substitution and rate heterogeneity. QUARTET PUZZLING TREE Support for the internal branches of the unrooted quartet puzzling tree topology is shown in percent. This quartet puzzling tree is not completely resolved! :---MYG_PHYCA : :100:---GLB5_PETMA : : :100: :---LGB2_LUPLU : : : : :---HBA_HUMAN : :100: : :---HBA_HORSE : :-----------HBB_HORSE : :-----------HBB_HUMAN Quartet puzzling tree (in CLUSTAL W notation): (HBB_HUMAN,((MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)100,(HBA_HUMAN, HBA_HORSE)100)100,HBB_HORSE); BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) ****... : 1000 **..... : 1000 **..*** : 1000 Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen) *****.. : 347 Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen) ****..* : 331 ****.*. : 322 MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :-------------5 MYG_PHYCA :-------8 : :-------6 GLB5_PETMA : : : :------------------7 LGB2_LUPLU :-------10 : : :-3 HBA_HUMAN : :-----9 : :--4 HBA_HORSE : :--2 HBB_HORSE : :-1 HBB_HUMAN branch length S.E. branch length S.E. HBB_HUMAN 1 0.05028 0.03102 8 0.44299 0.11946 HBB_HORSE 2 0.11946 0.03740 9 0.25788 0.08204 HBA_HUMAN 3 0.02934 0.02189 10 0.57110 0.10504 HBA_HORSE 4 0.09430 0.03146 MYG_PHYCA 5 1.11230 0.17628 GLB5_PETMA 6 0.59340 0.11994 11 iterations until convergence LGB2_LUPLU 7 1.46501 0.22199 log L: -1699.78 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): (HBB_HUMAN:0.05028,((MYG_PHYCA:1.11230,GLB5_PETMA:0.59340,LGB2_LUPLU:1.46501) 100:0.44299,(HBA_HUMAN:0.02934,HBA_HORSE:0.09430)100:0.25788)100:0.57110, HBB_HORSE:0.11946); TIME STAMP tree-puzzle-5.2/tests/check-qp-hky-clock-nucl0000644000076400001440000002703310073365717014746 TREE-PUZZLE Input file name: qp-hky-clock-nucl.nucl Type of analysis: tree reconstruction Parameter estimation: approximate (faster) Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) Standard errors (S.E.) are obtained by the curvature method. The upper and lower bounds of an approximate 95% confidence interval for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. SEQUENCE ALIGNMENT Input data: 8 sequences with 116 nucleotide sites Number of constant sites: 66 (= 56.9% of all sites) Number of site patterns: 54 Number of constant site patterns: 4 (= 7.4% of all site patterns) SUBSTITUTION PROCESS Model of substitution: HKY (Hasegawa et al. 1985) Transition/transversion parameter (estimated from data set): 1.51 (S.E. 0.28) Rate matrix R (parameters restricted to selected model): A-C rate: 1.00000 A-G rate: 2.98614 A-T rate: 1.00000 C-G rate: 1.00000 C-T rate: 2.98614 G-T rate: 1.00000 Nucleotide frequencies (estimated from data set): pi(A) = 26.6% pi(C) = 30.6% pi(G) = 12.0% pi(T) = 30.7% Expected transition/transversion ratio: 1.60 Expected pyrimidine transition/purine transition ratio: 2.95 AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) gaps wildcards sum % sequence Thylacinus 0 0 0 0.00% Sarcophilu 0 0 0 0.00% Dasyurus 0 1 1 0.86% Echymipera 0 0 0 0.00% Trichosuru 0 0 0 0.00% Phalanger 0 0 0 0.00% Philander 0 0 0 0.00% Bos 0 0 0 0.00% ------------------------------------------------------- Sum 0 1 1 0.11% The table above shows the amount of gaps ('-') and other 'wildcard' characters ('X', '?', etc.) and their percentage of the 116 columns in the alignment. Sequences with more than 50% ambiguous characters are marked with a '!' and should be checked, whether they have sufficient overlap to other sequences. Sequences with 100% ambiguous characters do not hold any phylogenetic information and had to be discarded from the analysis. SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) 5% chi-square test p-value Thylacinus passed 90.89% Sarcophilu passed 93.32% Dasyurus passed 98.01% Echymipera passed 92.83% Trichosuru passed 90.41% Phalanger passed 86.09% Philander passed 66.19% Bos passed 60.02% The chi-square tests compares the nucleotide composition of each sequence to the frequency distribution assumed in the maximum likelihood model. IDENTICAL SEQUENCES The sequences in each of the following groups are all identical. To speed up computation please remove all but one of each group from the data set. All sequences are unique. MAXIMUM LIKELIHOOD DISTANCES Maximum likelihood distances are computed using the selected model of substitution and rate heterogeneity. 8 Thylacinus 0.00000 0.25562 0.22032 0.24509 0.26007 0.24938 0.22246 0.23734 Sarcophilu 0.25562 0.00000 0.13169 0.26969 0.28414 0.32680 0.26008 0.29786 Dasyurus 0.22032 0.13169 0.00000 0.20032 0.24821 0.25234 0.17801 0.23883 Echymipera 0.24509 0.26969 0.20032 0.00000 0.29531 0.33871 0.23041 0.27215 Trichosuru 0.26007 0.28414 0.24821 0.29531 0.00000 0.21136 0.28562 0.27148 Phalanger 0.24938 0.32680 0.25234 0.33871 0.21136 0.00000 0.29036 0.33042 Philander 0.22246 0.26008 0.17801 0.23041 0.28562 0.29036 0.00000 0.22452 Bos 0.23734 0.29786 0.23883 0.27215 0.27148 0.33042 0.22452 0.00000 Average distance (over all possible pairs of sequences): 0.25459 minimum : 0.13169, maximum : 0.33871 variance : 0.00207, std.dev. : 0.04544 RATE HETEROGENEITY Model of rate heterogeneity: uniform rate QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) name | resolved | partly resolved | unresolved | sum -------------------------------------------------------------------------- Thylacinus 22 [ 62.86%] 4 [ 11.43%] 9 [ 25.71%] 35 Sarcophilu 27 [ 77.14%] 1 [ 2.86%] 7 [ 20.00%] 35 Dasyurus 27 [ 77.14%] 4 [ 11.43%] 4 [ 11.43%] 35 Echymipera 20 [ 57.14%] 4 [ 11.43%] 11 [ 31.43%] 35 Trichosuru 27 [ 77.14%] 2 [ 5.71%] 6 [ 17.14%] 35 Phalanger 28 [ 80.00%] 3 [ 8.57%] 4 [ 11.43%] 35 Philander 25 [ 71.43%] 6 [ 17.14%] 4 [ 11.43%] 35 Bos 20 [ 57.14%] 4 [ 11.43%] 11 [ 31.43%] 35 -------------------------------------------------------------------------- #quartets : 49 [ 70.00%] 7 [ 10.00%] 14 [ 20.00%] 70 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage relative to the number of times the sequence occurs in the list of quartets (i.e. 35 quartets out of 70 in total). In fully resolved quartet one single topology is supported, while for partially resolved quartets two and for completely unresolved quartets none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. Note: Because 4 sequences are involved in one quartet numbers add up to a four-fold of the existing quartets. Hint: The overall numbers in the last row give information about the phylogenetic content of the dataset. The higher the percentage of partially and unresolved quartets, the lower the content of phylogenetic information. This can be visualized in more detail by likelihood mapping analysis. TREE SEARCH Quartet puzzling is used to choose from the possible tree topologies and to simultaneously infer support values for internal branches. Number of puzzling steps: 1000 Analysed quartets: 70 Fully resolved quartets: 49 (= 70.0%) Partly resolved quartets: 7 (= 10.0%) Unresolved quartets: 14 (= 20.0%) Quartet trees are based on approximate maximum likelihood values using the selected model of substitution and rate heterogeneity. QUARTET PUZZLING TREE Support for the internal branches of the unrooted quartet puzzling tree topology is shown in percent. This quartet puzzling tree is not completely resolved! :---Trichosuru :-----97: : :---Phalanger : : :---Sarcophilu : :-98: : : :---Dasyurus : : :-71: :---Philander : :-65: : : :---Bos : : : :-------Echymipera : :-----------Thylacinus Quartet puzzling tree (in CLUSTAL W notation): (Thylacinus,(Trichosuru,Phalanger)97,((Sarcophilu,Dasyurus)98, (Philander,Bos)65,Echymipera)71); BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) *..***** : 981 ****..** : 971 *...**.. : 713 ******.. : 649 Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen) *...**** : 426 Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen) ***.**.. : 347 ***.**.* : 150 *...**.* : 131 *..***.. : 87 *..*..** : 81 *.....** : 72 ****..*. : 55 ***.***. : 37 ****.... : 36 *..***.* : 36 ***..... : 31 *.....*. : 28 *...***. : 27 *......* : 27 *....*.. : 26 *..*.... : 21 **..**** : 16 ***...** : 14 *..*..*. : 13 *..****. : 12 (6 other less frequent bipartitions not shown) MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :---------5 Trichosuru :------9 : :----------6 Phalanger : : :-----------2 Sarcophilu : :-------10 : : :-3 Dasyurus :-----12 : : :--------7 Philander : :----11 : : :-----------8 Bos : : : :------------4 Echymipera : :---------1 Thylacinus branch length S.E. branch length S.E. Thylacinus 1 0.11024 0.03812 9 0.05953 0.03382 Sarcophilu 2 0.13180 0.03734 10 0.08585 0.03452 Dasyurus 3 0.00572 0.01273 11 0.04220 0.02513 Echymipera 4 0.13997 0.04108 12 0.05457 0.02998 Trichosuru 5 0.10654 0.03770 Phalanger 6 0.12258 0.04064 Philander 7 0.08995 0.03428 8 iterations until convergence Bos 8 0.13479 0.04095 log L: -603.37 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): (Thylacinus:0.11024,(Trichosuru:0.10654,Phalanger:0.12258)97:0.05953, ((Sarcophilu:0.13180,Dasyurus:0.00572)98:0.08585,(Philander:0.08995, Bos:0.13479)65:0.04220,Echymipera:0.13997)71:0.05457); MAXIMUM LIKELIHOOD BRANCH LENGTHS OF CONSENSUS TREE (WITH CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. Root located at branch: 1 "Thylacinus" (automatic search) If the automatic search misplaces the root please rerun the analysis (rename "outtree" to "intree") and select location of root manually! :---------5 Trichosuru :-----9 : :---------6 Phalanger : : :-----2 Sarcophilu : :------10 : : :-----3 Dasyurus :--12 : : :--------7 Philander : :---11 : : :--------8 Bos : : : :-----------4 Echymipera : :------------1 Thylacinus Tree drawn as unrooted tree for better comparison with non-clock tree! branch length nc/c branch length nc/c (= non-clock/clock) Thylacinus 1 0.14706 0.750 9 0.04504 1.322 Sarcophilu 2 0.06189 2.130 10 0.06663 1.288 Dasyurus 3 0.06189 0.092 11 0.03304 1.277 Echymipera 4 0.12852 1.089 12 0.01851 2.948 Trichosuru 5 0.10199 1.045 Phalanger 6 0.10199 1.202 Philander 7 0.09549 0.942 6 iterations until convergence Bos 8 0.09549 1.412 log L: -610.75 height S.E. of node common to branches 0.10199 0.01922 9 5 6 0.06189 0.01495 10 2 3 0.09549 0.01498 11 7 8 0.12852 0.01108 12 10 11 4 0.14704 0.01235 1 9 12 0.14705 0.02366 of root at branch 1 Rooted consensus tree with clocklike maximum likelihood branch lengths (in CLUSTAL W notation): (Thylacinus:0.14705,((Trichosuru:0.10199,Phalanger:0.10199)97:0.04504 ,((Sarcophilu:0.06189,Dasyurus:0.06189)98:0.06663,(Philander:0.09549, Bos:0.09549)65:0.03304,Echymipera:0.12852)71:0.01851):0.00001); MOLECULAR CLOCK LIKELIHOOD RATIO TEST log L without clock: -603.37 (independent branch parameters: 12) log L with clock: -610.75 (independent branch parameters: 6) Likelihood ratio test statistic delta: 14.77 Degress of freedom of chi-square distribution: 6 Critical significance level: 2.22% The simpler (clocklike) tree is rejected on a significance level of 5%. The log-likelihood of the more complex (no clock) tree is significantly increased. Please take care that the correct root is used! TIME STAMP tree-puzzle-5.2/tests/qp-wag-prot.test0000755000076400001440000001622410073365716013570 #! /bin/sh # # template-test # # # Part of TREE-PUZZLE 5.2 (July 2004) # # (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler # (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, # M. Vingron, and Arndt von Haeseler # (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler # # All parts of the source except where indicated are distributed under # the GNU public licence. See http://www.opensource.org for details. # # ($Id$) # fname=`echo $0 | sed 's/.*\///'` GENERATE=0 TESTTYPE="Testing: " if test 0 -ne $# then case "$1" in -g*) GENERATE=1 TESTTYPE="Generating: " ;; *) echo "Usage: $fname [-g] " echo echo " Test a TREE-PUZZLE scenario." echo " With -g no test is performed, but the " echo " template for a future test is created." echo exit 1 ;; esac fi ########################################################################## TEST_PREF=`echo $fname | sed s/\.test//` INUTREE=${TEST_PREF}.trees INCTREE=${TEST_PREF}.ctrees PARAMS=${TEST_PREF}.param # default DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees # # data type # case "$TEST_PREF" in *-nucl) TESTTYPE="${TESTTYPE}nucleotide data" DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees echo d > $PARAMS case "$TEST_PREF" in *-hky*) TESTTYPE="${TESTTYPE}, HKY" ;; *-tn*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS ;; *-gtr*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS echo m >> $PARAMS ;; *-sh*) TESTTYPE="${TESTTYPE}, SH" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-prot) TESTTYPE="${TESTTYPE}protein data" DATA=prot INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/globin.a INUTREESOURCE=../data/globin.trees INCTREESOURCE=../data/globin.ctrees echo d > $PARAMS echo d >> $PARAMS case "$TEST_PREF" in *-dayhoff*) TESTTYPE="${TESTTYPE}, Dayhoff" echo m >> $PARAMS ;; *-jtt*) TESTTYPE="${TESTTYPE}, JTT" echo m >> $PARAMS echo m >> $PARAMS ;; *-mtrev*) TESTTYPE="${TESTTYPE}, mtREV" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-blosum*) TESTTYPE="${TESTTYPE}, BLOSUM" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-vt*) TESTTYPE="${TESTTYPE}, VT" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-wag*) TESTTYPE="${TESTTYPE}, WAG" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-bin) TESTTYPE="${TESTTYPE}binary data" DATA=bin INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/primates.b INUTREESOURCE=../data/primates.trees INCTREESOURCE=../data/primates.ctrees echo d > $PARAMS echo d >> $PARAMS echo d >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}default data, default model" ;; esac case "$TEST_PREF" in *-clock*) TESTTYPE="${TESTTYPE}, clock" echo z >> $PARAMS ;; esac case "$TEST_PREF" in *-rhet4*) TESTTYPE="${TESTTYPE}, rate heterogeneity (4 rates)" echo w >> $PARAMS echo c >> $PARAMS echo 4 >> $PARAMS ;; *-rhet*) TESTTYPE="${TESTTYPE}, rate heterogeneity" echo w >> $PARAMS ;; esac CHECK_PREF=check-$INFILE case "$TEST_PREF" in qp-*) TESTTYPE="${TESTTYPE}, quartet puzzling" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; lm-*) TESTTYPE="${TESTTYPE}, likelihood mapping" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo b >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; ut-*) TESTTYPE="${TESTTYPE}, user tree evaluation" cp $INFILESOURCE $INFILE cp $INUTREESOURCE $INUTREE RESULT_PREF=$INUTREE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INUTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; cons-*) TESTTYPE="${TESTTYPE}, consensus construction" cp $INFILESOURCE $INFILE cp $INCTREESOURCE $INCTREE RESULT_PREF=$INCTREE echo k >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INCTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; *) echo; echo "$TESTTYPE ($TEST_PREF)" echo UNKNOWN analysis type: test ignored exit 77 ;; esac if test $GENERATE == 1; then cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > check-${TEST_PREF} exit 0 else cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? exit $result fi tree-puzzle-5.2/tests/check-qp-jtt-prot0000644000076400001440000002057010073365723013702 TREE-PUZZLE Input file name: qp-jtt-prot.prot Type of analysis: tree reconstruction Parameter estimation: approximate (faster) Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) Standard errors (S.E.) are obtained by the curvature method. The upper and lower bounds of an approximate 95% confidence interval for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. SEQUENCE ALIGNMENT Input data: 7 sequences with 128 amino acid sites Number of constant sites: 7 (= 5.5% of all sites) Number of site patterns: 125 Number of constant site patterns: 5 (= 4.0% of all site patterns) SUBSTITUTION PROCESS Model of substitution: JTT (Jones et al. 1992) Amino acid frequencies (estimated from data set): pi(A) = 12.2% pi(R) = 2.3% pi(N) = 3.0% pi(D) = 4.9% pi(C) = 0.7% pi(Q) = 2.3% pi(E) = 5.4% pi(G) = 6.0% pi(H) = 5.8% pi(I) = 2.7% pi(L) = 12.5% pi(K) = 9.3% pi(M) = 1.3% pi(F) = 4.9% pi(P) = 2.6% pi(S) = 6.7% pi(T) = 4.5% pi(W) = 1.3% pi(Y) = 2.2% pi(V) = 9.4% AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) gaps wildcards sum % sequence HBB_HUMAN 0 0 0 0.00% HBB_HORSE 0 0 0 0.00% HBA_HUMAN 0 0 0 0.00% HBA_HORSE 0 0 0 0.00% MYG_PHYCA 0 0 0 0.00% GLB5_PETMA 0 0 0 0.00% LGB2_LUPLU 0 0 0 0.00% ------------------------------------------------------- Sum 0 0 0 0.00% The table above shows the amount of gaps ('-') and other 'wildcard' characters ('X', '?', etc.) and their percentage of the 128 columns in the alignment. Sequences with more than 50% ambiguous characters are marked with a '!' and should be checked, whether they have sufficient overlap to other sequences. Sequences with 100% ambiguous characters do not hold any phylogenetic information and had to be discarded from the analysis. SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) 5% chi-square test p-value HBB_HUMAN passed 92.31% HBB_HORSE passed 79.58% HBA_HUMAN passed 93.09% HBA_HORSE passed 81.20% MYG_PHYCA passed 33.23% GLB5_PETMA passed 19.11% LGB2_LUPLU passed 41.67% The chi-square tests compares the amino acid composition of each sequence to the frequency distribution assumed in the maximum likelihood model. WARNING: Result of chi-square test may not be valid because of small maximum likelihood frequencies and short sequence length! IDENTICAL SEQUENCES The sequences in each of the following groups are all identical. To speed up computation please remove all but one of each group from the data set. All sequences are unique. MAXIMUM LIKELIHOOD DISTANCES Maximum likelihood distances are computed using the selected model of substitution and rate heterogeneity. 7 HBB_HUMAN 0.00000 0.17343 0.93732 0.96340 2.06393 1.74159 2.60857 HBB_HORSE 0.17343 0.00000 0.97297 0.97742 2.03298 1.75271 2.65715 HBA_HUMAN 0.93732 0.97297 0.00000 0.12200 1.93956 1.25126 2.51688 HBA_HORSE 0.96340 0.97742 0.12200 0.00000 1.99570 1.34817 2.47562 MYG_PHYCA 2.06393 2.03298 1.93956 1.99570 0.00000 2.04426 2.69086 GLB5_PETMA 1.74159 1.75271 1.25126 1.34817 2.04426 0.00000 2.23399 LGB2_LUPLU 2.60857 2.65715 2.51688 2.47562 2.69086 2.23399 0.00000 Average distance (over all possible pairs of sequences): 1.69047 minimum : 0.12200, maximum : 2.69086 variance : 0.60537, std.dev. : 0.77805 RATE HETEROGENEITY Model of rate heterogeneity: uniform rate QUARTET STATISTICS (SEQUENCES IN INPUT ORDER) name | resolved | partly resolved | unresolved | sum -------------------------------------------------------------------------- HBB_HUMAN 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 HBB_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 HBA_HUMAN 19 [ 95.00%] 1 [ 5.00%] 0 [ 0.00%] 20 HBA_HORSE 19 [ 95.00%] 0 [ 0.00%] 1 [ 5.00%] 20 MYG_PHYCA 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 GLB5_PETMA 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 LGB2_LUPLU 16 [ 80.00%] 1 [ 5.00%] 3 [ 15.00%] 20 -------------------------------------------------------------------------- #quartets : 31 [ 88.57%] 1 [ 2.86%] 3 [ 8.57%] 35 The table shows the occurrences of fully resolved, partially, and completely unresolved quartets for each sequence and their percentage relative to the number of times the sequence occurs in the list of quartets (i.e. 20 quartets out of 35 in total). In fully resolved quartet one single topology is supported, while for partially resolved quartets two and for completely unresolved quartets none of the topologies (AB||CD, AC||BD, AD||BC) are favoured. Note: Because 4 sequences are involved in one quartet numbers add up to a four-fold of the existing quartets. Hint: The overall numbers in the last row give information about the phylogenetic content of the dataset. The higher the percentage of partially and unresolved quartets, the lower the content of phylogenetic information. This can be visualized in more detail by likelihood mapping analysis. TREE SEARCH Quartet puzzling is used to choose from the possible tree topologies and to simultaneously infer support values for internal branches. Number of puzzling steps: 1000 Analysed quartets: 35 Fully resolved quartets: 31 (= 88.6%) Partly resolved quartets: 1 (= 2.9%) Unresolved quartets: 3 (= 8.6%) Quartet trees are based on approximate maximum likelihood values using the selected model of substitution and rate heterogeneity. QUARTET PUZZLING TREE Support for the internal branches of the unrooted quartet puzzling tree topology is shown in percent. This quartet puzzling tree is not completely resolved! :---MYG_PHYCA : :100:---GLB5_PETMA : : :100: :---LGB2_LUPLU : : : : :---HBA_HUMAN : :100: : :---HBA_HORSE : :-----------HBB_HORSE : :-----------HBB_HUMAN Quartet puzzling tree (in CLUSTAL W notation): (HBB_HUMAN,((MYG_PHYCA,GLB5_PETMA,LGB2_LUPLU)100,(HBA_HUMAN, HBA_HORSE)100)100,HBB_HORSE); BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps. Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) ****... : 1000 **..... : 1000 **..*** : 1000 Congruent bipartitions occurred in 50% or less, not included in the consensus tree: (bipartition with sequences in input order : number of times seen) *****.. : 393 Incongruent bipartitions not included in the consensus tree: (bipartition with sequences in input order : number of times seen) ****.*. : 380 ****..* : 227 MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :--------------5 MYG_PHYCA :------8 : :-------6 GLB5_PETMA : : : :------------------7 LGB2_LUPLU :-------10 : : :-3 HBA_HUMAN : :----9 : :-4 HBA_HORSE : :--2 HBB_HORSE : :-1 HBB_HUMAN branch length S.E. branch length S.E. HBB_HUMAN 1 0.04638 0.03177 8 0.42254 0.12722 HBB_HORSE 2 0.12734 0.03889 9 0.25371 0.08572 HBA_HUMAN 3 0.02556 0.02189 10 0.61836 0.11268 HBA_HORSE 4 0.09595 0.03156 MYG_PHYCA 5 1.31230 0.21006 GLB5_PETMA 6 0.68479 0.13678 12 iterations until convergence LGB2_LUPLU 7 1.72936 0.26616 log L: -1707.74 Consensus tree with maximum likelihood branch lengths (in CLUSTAL W notation): (HBB_HUMAN:0.04638,((MYG_PHYCA:1.31230,GLB5_PETMA:0.68479,LGB2_LUPLU:1.72936) 100:0.42254,(HBA_HUMAN:0.02556,HBA_HORSE:0.09595)100:0.25371)100:0.61836, HBB_HORSE:0.12734); TIME STAMP tree-puzzle-5.2/tests/qp-clock.test0000755000076400001440000001622410073365716013123 #! /bin/sh # # template-test # # # Part of TREE-PUZZLE 5.2 (July 2004) # # (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler # (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, # M. Vingron, and Arndt von Haeseler # (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler # # All parts of the source except where indicated are distributed under # the GNU public licence. See http://www.opensource.org for details. # # ($Id$) # fname=`echo $0 | sed 's/.*\///'` GENERATE=0 TESTTYPE="Testing: " if test 0 -ne $# then case "$1" in -g*) GENERATE=1 TESTTYPE="Generating: " ;; *) echo "Usage: $fname [-g] " echo echo " Test a TREE-PUZZLE scenario." echo " With -g no test is performed, but the " echo " template for a future test is created." echo exit 1 ;; esac fi ########################################################################## TEST_PREF=`echo $fname | sed s/\.test//` INUTREE=${TEST_PREF}.trees INCTREE=${TEST_PREF}.ctrees PARAMS=${TEST_PREF}.param # default DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees # # data type # case "$TEST_PREF" in *-nucl) TESTTYPE="${TESTTYPE}nucleotide data" DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees echo d > $PARAMS case "$TEST_PREF" in *-hky*) TESTTYPE="${TESTTYPE}, HKY" ;; *-tn*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS ;; *-gtr*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS echo m >> $PARAMS ;; *-sh*) TESTTYPE="${TESTTYPE}, SH" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-prot) TESTTYPE="${TESTTYPE}protein data" DATA=prot INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/globin.a INUTREESOURCE=../data/globin.trees INCTREESOURCE=../data/globin.ctrees echo d > $PARAMS echo d >> $PARAMS case "$TEST_PREF" in *-dayhoff*) TESTTYPE="${TESTTYPE}, Dayhoff" echo m >> $PARAMS ;; *-jtt*) TESTTYPE="${TESTTYPE}, JTT" echo m >> $PARAMS echo m >> $PARAMS ;; *-mtrev*) TESTTYPE="${TESTTYPE}, mtREV" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-blosum*) TESTTYPE="${TESTTYPE}, BLOSUM" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-vt*) TESTTYPE="${TESTTYPE}, VT" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-wag*) TESTTYPE="${TESTTYPE}, WAG" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-bin) TESTTYPE="${TESTTYPE}binary data" DATA=bin INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/primates.b INUTREESOURCE=../data/primates.trees INCTREESOURCE=../data/primates.ctrees echo d > $PARAMS echo d >> $PARAMS echo d >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}default data, default model" ;; esac case "$TEST_PREF" in *-clock*) TESTTYPE="${TESTTYPE}, clock" echo z >> $PARAMS ;; esac case "$TEST_PREF" in *-rhet4*) TESTTYPE="${TESTTYPE}, rate heterogeneity (4 rates)" echo w >> $PARAMS echo c >> $PARAMS echo 4 >> $PARAMS ;; *-rhet*) TESTTYPE="${TESTTYPE}, rate heterogeneity" echo w >> $PARAMS ;; esac CHECK_PREF=check-$INFILE case "$TEST_PREF" in qp-*) TESTTYPE="${TESTTYPE}, quartet puzzling" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; lm-*) TESTTYPE="${TESTTYPE}, likelihood mapping" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo b >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; ut-*) TESTTYPE="${TESTTYPE}, user tree evaluation" cp $INFILESOURCE $INFILE cp $INUTREESOURCE $INUTREE RESULT_PREF=$INUTREE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INUTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; cons-*) TESTTYPE="${TESTTYPE}, consensus construction" cp $INFILESOURCE $INFILE cp $INCTREESOURCE $INCTREE RESULT_PREF=$INCTREE echo k >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INCTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; *) echo; echo "$TESTTYPE ($TEST_PREF)" echo UNKNOWN analysis type: test ignored exit 77 ;; esac if test $GENERATE == 1; then cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > check-${TEST_PREF} exit 0 else cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? exit $result fi tree-puzzle-5.2/tests/cons-pure-prot.test0000755000076400001440000001622410073365716014307 #! /bin/sh # # template-test # # # Part of TREE-PUZZLE 5.2 (July 2004) # # (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler # (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, # M. Vingron, and Arndt von Haeseler # (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler # # All parts of the source except where indicated are distributed under # the GNU public licence. See http://www.opensource.org for details. # # ($Id$) # fname=`echo $0 | sed 's/.*\///'` GENERATE=0 TESTTYPE="Testing: " if test 0 -ne $# then case "$1" in -g*) GENERATE=1 TESTTYPE="Generating: " ;; *) echo "Usage: $fname [-g] " echo echo " Test a TREE-PUZZLE scenario." echo " With -g no test is performed, but the " echo " template for a future test is created." echo exit 1 ;; esac fi ########################################################################## TEST_PREF=`echo $fname | sed s/\.test//` INUTREE=${TEST_PREF}.trees INCTREE=${TEST_PREF}.ctrees PARAMS=${TEST_PREF}.param # default DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees # # data type # case "$TEST_PREF" in *-nucl) TESTTYPE="${TESTTYPE}nucleotide data" DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees echo d > $PARAMS case "$TEST_PREF" in *-hky*) TESTTYPE="${TESTTYPE}, HKY" ;; *-tn*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS ;; *-gtr*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS echo m >> $PARAMS ;; *-sh*) TESTTYPE="${TESTTYPE}, SH" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-prot) TESTTYPE="${TESTTYPE}protein data" DATA=prot INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/globin.a INUTREESOURCE=../data/globin.trees INCTREESOURCE=../data/globin.ctrees echo d > $PARAMS echo d >> $PARAMS case "$TEST_PREF" in *-dayhoff*) TESTTYPE="${TESTTYPE}, Dayhoff" echo m >> $PARAMS ;; *-jtt*) TESTTYPE="${TESTTYPE}, JTT" echo m >> $PARAMS echo m >> $PARAMS ;; *-mtrev*) TESTTYPE="${TESTTYPE}, mtREV" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-blosum*) TESTTYPE="${TESTTYPE}, BLOSUM" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-vt*) TESTTYPE="${TESTTYPE}, VT" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-wag*) TESTTYPE="${TESTTYPE}, WAG" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-bin) TESTTYPE="${TESTTYPE}binary data" DATA=bin INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/primates.b INUTREESOURCE=../data/primates.trees INCTREESOURCE=../data/primates.ctrees echo d > $PARAMS echo d >> $PARAMS echo d >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}default data, default model" ;; esac case "$TEST_PREF" in *-clock*) TESTTYPE="${TESTTYPE}, clock" echo z >> $PARAMS ;; esac case "$TEST_PREF" in *-rhet4*) TESTTYPE="${TESTTYPE}, rate heterogeneity (4 rates)" echo w >> $PARAMS echo c >> $PARAMS echo 4 >> $PARAMS ;; *-rhet*) TESTTYPE="${TESTTYPE}, rate heterogeneity" echo w >> $PARAMS ;; esac CHECK_PREF=check-$INFILE case "$TEST_PREF" in qp-*) TESTTYPE="${TESTTYPE}, quartet puzzling" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; lm-*) TESTTYPE="${TESTTYPE}, likelihood mapping" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo b >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; ut-*) TESTTYPE="${TESTTYPE}, user tree evaluation" cp $INFILESOURCE $INFILE cp $INUTREESOURCE $INUTREE RESULT_PREF=$INUTREE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INUTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; cons-*) TESTTYPE="${TESTTYPE}, consensus construction" cp $INFILESOURCE $INFILE cp $INCTREESOURCE $INCTREE RESULT_PREF=$INCTREE echo k >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INCTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; *) echo; echo "$TESTTYPE ($TEST_PREF)" echo UNKNOWN analysis type: test ignored exit 77 ;; esac if test $GENERATE == 1; then cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > check-${TEST_PREF} exit 0 else cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? exit $result fi tree-puzzle-5.2/tests/check-lm-pure-prot0000644000076400001440000001265210073365741014046 TREE-PUZZLE Input file name: lm-pure-prot.prot Type of analysis: likelihood mapping Parameter estimation: approximate (faster) Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) Standard errors (S.E.) are obtained by the curvature method. The upper and lower bounds of an approximate 95% confidence interval for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. SEQUENCE ALIGNMENT Input data: 7 sequences with 128 amino acid sites Number of constant sites: 7 (= 5.5% of all sites) Number of site patterns: 125 Number of constant site patterns: 5 (= 4.0% of all site patterns) SUBSTITUTION PROCESS Model of substitution: Dayhoff (Dayhoff et al. 1978) Amino acid frequencies (estimated from data set): pi(A) = 12.2% pi(R) = 2.3% pi(N) = 3.0% pi(D) = 4.9% pi(C) = 0.7% pi(Q) = 2.3% pi(E) = 5.4% pi(G) = 6.0% pi(H) = 5.8% pi(I) = 2.7% pi(L) = 12.5% pi(K) = 9.3% pi(M) = 1.3% pi(F) = 4.9% pi(P) = 2.6% pi(S) = 6.7% pi(T) = 4.5% pi(W) = 1.3% pi(Y) = 2.2% pi(V) = 9.4% AMBIGUOUS CHARACTERS IN THE SEQUENCE (SEQUENCES IN INPUT ORDER) gaps wildcards sum % sequence HBB_HUMAN 0 0 0 0.00% HBB_HORSE 0 0 0 0.00% HBA_HUMAN 0 0 0 0.00% HBA_HORSE 0 0 0 0.00% MYG_PHYCA 0 0 0 0.00% GLB5_PETMA 0 0 0 0.00% LGB2_LUPLU 0 0 0 0.00% ------------------------------------------------------- Sum 0 0 0 0.00% The table above shows the amount of gaps ('-') and other 'wildcard' characters ('X', '?', etc.) and their percentage of the 128 columns in the alignment. Sequences with more than 50% ambiguous characters are marked with a '!' and should be checked, whether they have sufficient overlap to other sequences. Sequences with 100% ambiguous characters do not hold any phylogenetic information and had to be discarded from the analysis. SEQUENCE COMPOSITION (SEQUENCES IN INPUT ORDER) 5% chi-square test p-value HBB_HUMAN passed 92.31% HBB_HORSE passed 79.58% HBA_HUMAN passed 93.09% HBA_HORSE passed 81.20% MYG_PHYCA passed 33.23% GLB5_PETMA passed 19.11% LGB2_LUPLU passed 41.67% The chi-square tests compares the amino acid composition of each sequence to the frequency distribution assumed in the maximum likelihood model. WARNING: Result of chi-square test may not be valid because of small maximum likelihood frequencies and short sequence length! IDENTICAL SEQUENCES The sequences in each of the following groups are all identical. To speed up computation please remove all but one of each group from the data set. All sequences are unique. MAXIMUM LIKELIHOOD DISTANCES Maximum likelihood distances are computed using the selected model of substitution and rate heterogeneity. 7 HBB_HUMAN 0.00000 0.17425 0.96068 0.99267 2.12932 1.77231 2.78644 HBB_HORSE 0.17425 0.00000 1.01062 1.02118 2.09456 1.78465 2.86187 HBA_HUMAN 0.96068 1.01062 0.00000 0.12147 1.93540 1.30123 2.54730 HBA_HORSE 0.99267 1.02118 0.12147 0.00000 2.00515 1.39193 2.51172 MYG_PHYCA 2.12932 2.09456 1.93540 2.00515 0.00000 2.12347 2.79386 GLB5_PETMA 1.77231 1.78465 1.30123 1.39193 2.12347 0.00000 2.18272 LGB2_LUPLU 2.78644 2.86187 2.54730 2.51172 2.79386 2.18272 0.00000 Average distance (over all possible pairs of sequences): 1.73823 minimum : 0.12147, maximum : 2.86187 variance : 0.65214, std.dev. : 0.80755 RATE HETEROGENEITY Model of rate heterogeneity: uniform rate LIKELIHOOD MAPPING ANALYSIS Number of quartets: 35 (all possible) Quartet trees are based on approximate maximum likelihood values using the selected model of substitution and rate heterogeneity. Sequences are not grouped in clusters. LIKELIHOOD MAPPING STATISTICS Occupancies of the three areas 1, 2, 3: /\ / \ / \ / 1 \ / \ / \ / \ / \ / \/ \ / 3 : 2 \ / : \ /__________________\ Number of quartets in region 1: 14 (= 40.0%) Number of quartets in region 2: 11 (= 31.4%) Number of quartets in region 3: 10 (= 28.6%) Occupancies of the seven areas 1, 2, 3, 4, 5, 6, 7: /\ / \ / 1 \ / \ / \ / /\ \ / 6 / \ 4 \ / / 7 \ \ / \ /______\ / \ / 3 : 5 : 2 \ /__________________\ Number of quartets in region 1: 12 (= 34.3%) left: 3 right: 9 Number of quartets in region 2: 11 (= 31.4%) bottom: 3 top: 8 Number of quartets in region 3: 9 (= 25.7%) bottom: 4 top: 5 Number of quartets in region 4: 0 (= 0.0%) bottom: 0 top: 0 Number of quartets in region 5: 0 (= 0.0%) left: 0 right: 0 Number of quartets in region 6: 0 (= 0.0%) bottom: 0 top: 0 Number of quartets in region 7: 3 (= 8.6%) TIME STAMP tree-puzzle-5.2/tests/qp-pure-bin.test0000755000076400001440000001622410073365716013551 #! /bin/sh # # template-test # # # Part of TREE-PUZZLE 5.2 (July 2004) # # (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler # (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, # M. Vingron, and Arndt von Haeseler # (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler # # All parts of the source except where indicated are distributed under # the GNU public licence. See http://www.opensource.org for details. # # ($Id$) # fname=`echo $0 | sed 's/.*\///'` GENERATE=0 TESTTYPE="Testing: " if test 0 -ne $# then case "$1" in -g*) GENERATE=1 TESTTYPE="Generating: " ;; *) echo "Usage: $fname [-g] " echo echo " Test a TREE-PUZZLE scenario." echo " With -g no test is performed, but the " echo " template for a future test is created." echo exit 1 ;; esac fi ########################################################################## TEST_PREF=`echo $fname | sed s/\.test//` INUTREE=${TEST_PREF}.trees INCTREE=${TEST_PREF}.ctrees PARAMS=${TEST_PREF}.param # default DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees # # data type # case "$TEST_PREF" in *-nucl) TESTTYPE="${TESTTYPE}nucleotide data" DATA=nucl INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/marswolf.n INUTREESOURCE=../data/marswolf.trees INCTREESOURCE=../data/marswolf.ctrees echo d > $PARAMS case "$TEST_PREF" in *-hky*) TESTTYPE="${TESTTYPE}, HKY" ;; *-tn*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS ;; *-gtr*) TESTTYPE="${TESTTYPE}, TN" echo m >> $PARAMS echo m >> $PARAMS ;; *-sh*) TESTTYPE="${TESTTYPE}, SH" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-prot) TESTTYPE="${TESTTYPE}protein data" DATA=prot INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/globin.a INUTREESOURCE=../data/globin.trees INCTREESOURCE=../data/globin.ctrees echo d > $PARAMS echo d >> $PARAMS case "$TEST_PREF" in *-dayhoff*) TESTTYPE="${TESTTYPE}, Dayhoff" echo m >> $PARAMS ;; *-jtt*) TESTTYPE="${TESTTYPE}, JTT" echo m >> $PARAMS echo m >> $PARAMS ;; *-mtrev*) TESTTYPE="${TESTTYPE}, mtREV" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-blosum*) TESTTYPE="${TESTTYPE}, BLOSUM" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-vt*) TESTTYPE="${TESTTYPE}, VT" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *-wag*) TESTTYPE="${TESTTYPE}, WAG" echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS echo m >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}, default model" esac ;; *-bin) TESTTYPE="${TESTTYPE}binary data" DATA=bin INFILE=${TEST_PREF}.${DATA} INFILESOURCE=../data/primates.b INUTREESOURCE=../data/primates.trees INCTREESOURCE=../data/primates.ctrees echo d > $PARAMS echo d >> $PARAMS echo d >> $PARAMS ;; *) TESTTYPE="${TESTTYPE}default data, default model" ;; esac case "$TEST_PREF" in *-clock*) TESTTYPE="${TESTTYPE}, clock" echo z >> $PARAMS ;; esac case "$TEST_PREF" in *-rhet4*) TESTTYPE="${TESTTYPE}, rate heterogeneity (4 rates)" echo w >> $PARAMS echo c >> $PARAMS echo 4 >> $PARAMS ;; *-rhet*) TESTTYPE="${TESTTYPE}, rate heterogeneity" echo w >> $PARAMS ;; esac CHECK_PREF=check-$INFILE case "$TEST_PREF" in qp-*) TESTTYPE="${TESTTYPE}, quartet puzzling" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; lm-*) TESTTYPE="${TESTTYPE}, likelihood mapping" cp $INFILESOURCE $INFILE RESULT_PREF=$INFILE echo b >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1 ;; ut-*) TESTTYPE="${TESTTYPE}, user tree evaluation" cp $INFILESOURCE $INFILE cp $INUTREESOURCE $INUTREE RESULT_PREF=$INUTREE echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INUTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; cons-*) TESTTYPE="${TESTTYPE}, consensus construction" cp $INFILESOURCE $INFILE cp $INCTREESOURCE $INCTREE RESULT_PREF=$INCTREE echo k >> $PARAMS echo y >> $PARAMS echo; echo "$TESTTYPE ($TEST_PREF)" ../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INCTREE} < $PARAMS > ${INFILE}.out 2>&1 ;; *) echo; echo "$TESTTYPE ($TEST_PREF)" echo UNKNOWN analysis type: test ignored exit 77 ;; esac if test $GENERATE == 1; then cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > check-${TEST_PREF} exit 0 else cat ${RESULT_PREF}.puzzle \ | grep -v "^Date and time" \ | grep -v "^Runtime (" \ | sed "s/$VERSION//g" \ > ${RESULT_PREF}.clean diff ${RESULT_PREF}.clean check-${TEST_PREF} result=$? exit $result fi tree-puzzle-5.2/README0000644000076400001440000000302610070674527010220 TREE-PUZZLE 5.2 TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. TREE-PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can also be calculated under the clock-assumption. In addition, TREE-PUZZLE offers a novel method, likelihood mapping, to investigate the support of a hypothesized internal branch without computing an overall tree and to visualize the phylogenetic content of a sequence alignment. TREE-PUZZLE also conducts a number of statistical tests on the data set (chi-square test for homogeneity of base composition, likelihood ratio to test the clock hypothesis, Kishino-Hasegawa test). The models of substitution provided by TREE-PUZZLE are TN, HKY, F84, SH for nucleotides, Dayhoff, JTT, mtREV24, BLOSUM 62, VT, WAG for amino acids, and F81 for two-state data. Rate heterogeneity is modelled by a discrete Gamma distribution and by allowing invariable sites. The corresponding parameters can be inferred from the data set. INSTALLATION For compile an intall instructions see INSTALL and doc/manual.html In most cases on UNIX machines the following should work (if the prefix is left out configure the executable are installed in /urs/local): sh ./configure --prefix=/usr/local make make install tree-puzzle-5.2/configure0000755000076400001440000047475010075305501011253 #! /bin/sh # Guess values for system-dependent variables and create Makefiles. # Generated by GNU Autoconf 2.53. # # Copyright 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001, 2002 # Free Software Foundation, Inc. # This configure script is free software; the Free Software Foundation # gives unlimited permission to copy, distribute and modify it. if expr a : '\(a\)' >/dev/null 2>&1; then as_expr=expr else as_expr=false fi ## --------------------- ## ## M4sh Initialization. ## ## --------------------- ## # Be Bourne compatible if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then emulate sh NULLCMD=: elif test -n "${BASH_VERSION+set}" && (set -o posix) >/dev/null 2>&1; then set -o posix fi # NLS nuisances. # Support unset when possible. if (FOO=FOO; unset FOO) >/dev/null 2>&1; then as_unset=unset else as_unset=false fi (set +x; test -n "`(LANG=C; export LANG) 2>&1`") && { $as_unset LANG || test "${LANG+set}" != set; } || { LANG=C; export LANG; } (set +x; test -n "`(LC_ALL=C; export LC_ALL) 2>&1`") && { $as_unset LC_ALL || test "${LC_ALL+set}" != set; } || { LC_ALL=C; export LC_ALL; } (set +x; test -n "`(LC_TIME=C; export LC_TIME) 2>&1`") && { $as_unset LC_TIME || test "${LC_TIME+set}" != set; } || { LC_TIME=C; export LC_TIME; } (set +x; test -n "`(LC_CTYPE=C; export LC_CTYPE) 2>&1`") && { $as_unset LC_CTYPE || test "${LC_CTYPE+set}" != set; } || { LC_CTYPE=C; export LC_CTYPE; } (set +x; test -n "`(LANGUAGE=C; export LANGUAGE) 2>&1`") && { $as_unset LANGUAGE || test "${LANGUAGE+set}" != set; } || { LANGUAGE=C; export LANGUAGE; } (set +x; test -n "`(LC_COLLATE=C; export LC_COLLATE) 2>&1`") && { $as_unset LC_COLLATE || test "${LC_COLLATE+set}" != set; } || { LC_COLLATE=C; export LC_COLLATE; } (set +x; test -n "`(LC_NUMERIC=C; export LC_NUMERIC) 2>&1`") && { $as_unset LC_NUMERIC || test "${LC_NUMERIC+set}" != set; } || { LC_NUMERIC=C; export LC_NUMERIC; } (set +x; test -n "`(LC_MESSAGES=C; export LC_MESSAGES) 2>&1`") && { $as_unset LC_MESSAGES || test "${LC_MESSAGES+set}" != set; } || { LC_MESSAGES=C; export LC_MESSAGES; } # Name of the executable. as_me=`(basename "$0") 2>/dev/null || $as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ X"$0" : 'X\(//\)$' \| \ X"$0" : 'X\(/\)$' \| \ . : '\(.\)' 2>/dev/null || echo X/"$0" | sed '/^.*\/\([^/][^/]*\)\/*$/{ s//\1/; q; } /^X\/\(\/\/\)$/{ s//\1/; q; } /^X\/\(\/\).*/{ s//\1/; q; } s/.*/./; q'` # PATH needs CR, and LINENO needs CR and PATH. # Avoid depending upon Character Ranges. as_cr_letters='abcdefghijklmnopqrstuvwxyz' as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' as_cr_Letters=$as_cr_letters$as_cr_LETTERS as_cr_digits='0123456789' as_cr_alnum=$as_cr_Letters$as_cr_digits # The user is always right. if test "${PATH_SEPARATOR+set}" != set; then echo "#! /bin/sh" >conftest.sh echo "exit 0" >>conftest.sh chmod +x conftest.sh if (PATH=".;."; conftest.sh) >/dev/null 2>&1; then PATH_SEPARATOR=';' else PATH_SEPARATOR=: fi rm -f conftest.sh fi as_lineno_1=$LINENO as_lineno_2=$LINENO as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null` test "x$as_lineno_1" != "x$as_lineno_2" && test "x$as_lineno_3" = "x$as_lineno_2" || { # Find who we are. 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It has an incompatible calling convention. : elif test $ac_prog = install && grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then # program-specific install script used by HP pwplus--don't use. : else ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c" break 3 fi fi done done ;; esac done fi if test "${ac_cv_path_install+set}" = set; then INSTALL=$ac_cv_path_install else # As a last resort, use the slow shell script. We don't cache a # path for INSTALL within a source directory, because that will # break other packages using the cache if that directory is # removed, or if the path is relative. INSTALL=$ac_install_sh fi fi echo "$as_me:$LINENO: result: $INSTALL" >&5 echo "${ECHO_T}$INSTALL" >&6 # Use test -z because SunOS4 sh mishandles braces in ${var-val}. # It thinks the first close brace ends the variable substitution. test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}' test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}' test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644' echo "$as_me:$LINENO: checking whether build environment is sane" >&5 echo $ECHO_N "checking whether build environment is sane... $ECHO_C" >&6 # Just in case sleep 1 echo timestamp > conftest.file # Do `set' in a subshell so we don't clobber the current shell's # arguments. Must try -L first in case configure is actually a # symlink; some systems play weird games with the mod time of symlinks # (eg FreeBSD returns the mod time of the symlink's containing # directory). if ( set X `ls -Lt $srcdir/configure conftest.file 2> /dev/null` if test "$*" = "X"; then # -L didn't work. set X `ls -t $srcdir/configure conftest.file` fi rm -f conftest.file if test "$*" != "X $srcdir/configure conftest.file" \ && test "$*" != "X conftest.file $srcdir/configure"; then # If neither matched, then we have a broken ls. This can happen # if, for instance, CONFIG_SHELL is bash and it inherits a # broken ls alias from the environment. This has actually # happened. Such a system could not be considered "sane". { { echo "$as_me:$LINENO: error: ls -t appears to fail. Make sure there is not a broken alias in your environment" >&5 echo "$as_me: error: ls -t appears to fail. Make sure there is not a broken alias in your environment" >&2;} { (exit 1); exit 1; }; } fi test "$2" = conftest.file ) then # Ok. : else { { echo "$as_me:$LINENO: error: newly created file is older than distributed files! Check your system clock" >&5 echo "$as_me: error: newly created file is older than distributed files! Check your system clock" >&2;} { (exit 1); exit 1; }; } fi echo "$as_me:$LINENO: result: yes" >&5 echo "${ECHO_T}yes" >&6 test "$program_prefix" != NONE && program_transform_name="s,^,$program_prefix,;$program_transform_name" # Use a double $ so make ignores it. test "$program_suffix" != NONE && program_transform_name="s,\$,$program_suffix,;$program_transform_name" # Double any \ or $. echo might interpret backslashes. # By default was `s,x,x', remove it if useless. cat <<\_ACEOF >conftest.sed s/[\\$]/&&/g;s/;s,x,x,$// _ACEOF program_transform_name=`echo $program_transform_name | sed -f conftest.sed` rm conftest.sed # expand $ac_aux_dir to an absolute path am_aux_dir=`cd $ac_aux_dir && pwd` test x"${MISSING+set}" = xset || MISSING="\${SHELL} $am_aux_dir/missing" # Use eval to expand $SHELL if eval "$MISSING --run true"; then am_missing_run="$MISSING --run " else am_missing_run= { echo "$as_me:$LINENO: WARNING: \`missing' script is too old or missing" >&5 echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;} fi for ac_prog in gawk mawk nawk awk do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_prog_AWK+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test -n "$AWK"; then ac_cv_prog_AWK="$AWK" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_AWK="$ac_prog" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done fi fi AWK=$ac_cv_prog_AWK if test -n "$AWK"; then echo "$as_me:$LINENO: result: $AWK" >&5 echo "${ECHO_T}$AWK" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi test -n "$AWK" && break done echo "$as_me:$LINENO: checking whether ${MAKE-make} sets \${MAKE}" >&5 echo $ECHO_N "checking whether ${MAKE-make} sets \${MAKE}... $ECHO_C" >&6 set dummy ${MAKE-make}; ac_make=`echo "$2" | sed 'y,./+-,__p_,'` if eval "test \"\${ac_cv_prog_make_${ac_make}_set+set}\" = set"; then echo $ECHO_N "(cached) $ECHO_C" >&6 else cat >conftest.make <<\_ACEOF all: @echo 'ac_maketemp="${MAKE}"' _ACEOF # GNU make sometimes prints "make[1]: Entering...", which would confuse us. eval `${MAKE-make} -f conftest.make 2>/dev/null | grep temp=` if test -n "$ac_maketemp"; then eval ac_cv_prog_make_${ac_make}_set=yes else eval ac_cv_prog_make_${ac_make}_set=no fi rm -f conftest.make fi if eval "test \"`echo '$ac_cv_prog_make_'${ac_make}_set`\" = yes"; then echo "$as_me:$LINENO: result: yes" >&5 echo "${ECHO_T}yes" >&6 SET_MAKE= else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 SET_MAKE="MAKE=${MAKE-make}" fi # test to see if srcdir already configured if test "`cd $srcdir && pwd`" != "`pwd`" && test -f $srcdir/config.status; then { { echo "$as_me:$LINENO: error: source directory already configured; run \"make distclean\" there first" >&5 echo "$as_me: error: source directory already configured; run \"make distclean\" there first" >&2;} { (exit 1); exit 1; }; } fi # Define the identity of the package. PACKAGE=tree-puzzle VERSION=5.2 cat >>confdefs.h <<_ACEOF #define PACKAGE "$PACKAGE" _ACEOF cat >>confdefs.h <<_ACEOF #define VERSION "$VERSION" _ACEOF # Some tools Automake needs. ACLOCAL=${ACLOCAL-"${am_missing_run}aclocal-${am__api_version}"} AUTOCONF=${AUTOCONF-"${am_missing_run}autoconf"} AUTOMAKE=${AUTOMAKE-"${am_missing_run}automake-${am__api_version}"} AUTOHEADER=${AUTOHEADER-"${am_missing_run}autoheader"} MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"} AMTAR=${AMTAR-"${am_missing_run}tar"} install_sh=${install_sh-"$am_aux_dir/install-sh"} # Installed binaries are usually stripped using `strip' when the user # run `make install-strip'. However `strip' might not be the right # tool to use in cross-compilation environments, therefore Automake # will honor the `STRIP' environment variable to overrule this program. if test "$cross_compiling" != no; then if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args. set dummy ${ac_tool_prefix}strip; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_prog_STRIP+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test -n "$STRIP"; then ac_cv_prog_STRIP="$STRIP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_STRIP="${ac_tool_prefix}strip" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done fi fi STRIP=$ac_cv_prog_STRIP if test -n "$STRIP"; then echo "$as_me:$LINENO: result: $STRIP" >&5 echo "${ECHO_T}$STRIP" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi fi if test -z "$ac_cv_prog_STRIP"; then ac_ct_STRIP=$STRIP # Extract the first word of "strip", so it can be a program name with args. set dummy strip; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test -n "$ac_ct_STRIP"; then ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_STRIP="strip" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done test -z "$ac_cv_prog_ac_ct_STRIP" && ac_cv_prog_ac_ct_STRIP=":" fi fi ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP if test -n "$ac_ct_STRIP"; then echo "$as_me:$LINENO: result: $ac_ct_STRIP" >&5 echo "${ECHO_T}$ac_ct_STRIP" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi STRIP=$ac_ct_STRIP else STRIP="$ac_cv_prog_STRIP" fi fi INSTALL_STRIP_PROGRAM="\${SHELL} \$(install_sh) -c -s" # We need awk for the "check" target. The system "awk" is bad on # some platforms. # Add the stamp file to the list of files AC keeps track of, # along with our hook. ac_config_headers="$ac_config_headers src/config.h" ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args. set dummy ${ac_tool_prefix}gcc; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_prog_CC+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_CC="${ac_tool_prefix}gcc" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then echo "$as_me:$LINENO: result: $CC" >&5 echo "${ECHO_T}$CC" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi fi if test -z "$ac_cv_prog_CC"; then ac_ct_CC=$CC # Extract the first word of "gcc", so it can be a program name with args. set dummy gcc; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_prog_ac_ct_CC+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test -n "$ac_ct_CC"; then ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_CC="gcc" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done fi fi ac_ct_CC=$ac_cv_prog_ac_ct_CC if test -n "$ac_ct_CC"; then echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 echo "${ECHO_T}$ac_ct_CC" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi CC=$ac_ct_CC else CC="$ac_cv_prog_CC" fi if test -z "$CC"; then if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args. set dummy ${ac_tool_prefix}cc; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_prog_CC+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_CC="${ac_tool_prefix}cc" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then echo "$as_me:$LINENO: result: $CC" >&5 echo "${ECHO_T}$CC" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi fi if test -z "$ac_cv_prog_CC"; then ac_ct_CC=$CC # Extract the first word of "cc", so it can be a program name with args. set dummy cc; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_prog_ac_ct_CC+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test -n "$ac_ct_CC"; then ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_CC="cc" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done fi fi ac_ct_CC=$ac_cv_prog_ac_ct_CC if test -n "$ac_ct_CC"; then echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 echo "${ECHO_T}$ac_ct_CC" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi CC=$ac_ct_CC else CC="$ac_cv_prog_CC" fi fi if test -z "$CC"; then # Extract the first word of "cc", so it can be a program name with args. set dummy cc; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_prog_CC+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. else ac_prog_rejected=no as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then ac_prog_rejected=yes continue fi ac_cv_prog_CC="cc" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done if test $ac_prog_rejected = yes; then # We found a bogon in the path, so make sure we never use it. set dummy $ac_cv_prog_CC shift if test $# != 0; then # We chose a different compiler from the bogus one. # However, it has the same basename, so the bogon will be chosen # first if we set CC to just the basename; use the full file name. shift set dummy "$as_dir/$ac_word" ${1+"$@"} shift ac_cv_prog_CC="$@" fi fi fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then echo "$as_me:$LINENO: result: $CC" >&5 echo "${ECHO_T}$CC" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi fi if test -z "$CC"; then if test -n "$ac_tool_prefix"; then for ac_prog in cl do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_prog_CC+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_CC="$ac_tool_prefix$ac_prog" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then echo "$as_me:$LINENO: result: $CC" >&5 echo "${ECHO_T}$CC" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi test -n "$CC" && break done fi if test -z "$CC"; then ac_ct_CC=$CC for ac_prog in cl do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_prog_ac_ct_CC+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test -n "$ac_ct_CC"; then ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_CC="$ac_prog" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done fi fi ac_ct_CC=$ac_cv_prog_ac_ct_CC if test -n "$ac_ct_CC"; then echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 echo "${ECHO_T}$ac_ct_CC" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi test -n "$ac_ct_CC" && break done CC=$ac_ct_CC fi fi test -z "$CC" && { { echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH" >&5 echo "$as_me: error: no acceptable C compiler found in \$PATH" >&2;} { (exit 1); exit 1; }; } # Provide some information about the compiler. echo "$as_me:$LINENO:" \ "checking for C compiler version" >&5 ac_compiler=`set X $ac_compile; echo $2` { (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 (eval $ac_compiler --version &5) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } { (eval echo "$as_me:$LINENO: \"$ac_compiler -v &5\"") >&5 (eval $ac_compiler -v &5) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } { (eval echo "$as_me:$LINENO: \"$ac_compiler -V &5\"") >&5 (eval $ac_compiler -V &5) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } cat >conftest.$ac_ext <<_ACEOF #line $LINENO "configure" #include "confdefs.h" #ifdef F77_DUMMY_MAIN # ifdef __cplusplus extern "C" # endif int F77_DUMMY_MAIN() { return 1; } #endif int main () { ; return 0; } _ACEOF ac_clean_files_save=$ac_clean_files ac_clean_files="$ac_clean_files a.out a.exe" # Try to create an executable without -o first, disregard a.out. # It will help us diagnose broken compilers, and finding out an intuition # of exeext. echo "$as_me:$LINENO: checking for C compiler default output" >&5 echo $ECHO_N "checking for C compiler default output... $ECHO_C" >&6 ac_link_default=`echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'` if { (eval echo "$as_me:$LINENO: \"$ac_link_default\"") >&5 (eval $ac_link_default) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; then # Find the output, starting from the most likely. 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INSTALL=$ac_install_sh fi fi echo "$as_me:$LINENO: result: $INSTALL" >&5 echo "${ECHO_T}$INSTALL" >&6 # Use test -z because SunOS4 sh mishandles braces in ${var-val}. # It thinks the first close brace ends the variable substitution. test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}' test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}' test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644' echo "$as_me:$LINENO: checking whether ${MAKE-make} sets \${MAKE}" >&5 echo $ECHO_N "checking whether ${MAKE-make} sets \${MAKE}... $ECHO_C" >&6 set dummy ${MAKE-make}; ac_make=`echo "$2" | sed 'y,./+-,__p_,'` if eval "test \"\${ac_cv_prog_make_${ac_make}_set+set}\" = set"; then echo $ECHO_N "(cached) $ECHO_C" >&6 else cat >conftest.make <<\_ACEOF all: @echo 'ac_maketemp="${MAKE}"' _ACEOF # GNU make sometimes prints "make[1]: Entering...", which would confuse us. eval `${MAKE-make} -f conftest.make 2>/dev/null | grep temp=` if test -n "$ac_maketemp"; then eval ac_cv_prog_make_${ac_make}_set=yes else eval ac_cv_prog_make_${ac_make}_set=no fi rm -f conftest.make fi if eval "test \"`echo '$ac_cv_prog_make_'${ac_make}_set`\" = yes"; then echo "$as_me:$LINENO: result: yes" >&5 echo "${ECHO_T}yes" >&6 SET_MAKE= else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 SET_MAKE="MAKE=${MAKE-make}" fi if test "$MPICC" != "" ; then # Extract the first word of "$MPICC", so it can be a program name with args. set dummy $MPICC; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_MPICC0+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $MPICC0 in [\\/]* | ?:[\\/]*) ac_cv_path_MPICC0="$MPICC0" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_MPICC0="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi MPICC0=$ac_cv_path_MPICC0 if test -n "$MPICC0"; then echo "$as_me:$LINENO: result: $MPICC0" >&5 echo "${ECHO_T}$MPICC0" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi fi # Extract the first word of "mpcc", so it can be a program name with args. set dummy mpcc; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_MPICC1+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $MPICC1 in [\\/]* | ?:[\\/]*) ac_cv_path_MPICC1="$MPICC1" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_MPICC1="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi MPICC1=$ac_cv_path_MPICC1 if test -n "$MPICC1"; then echo "$as_me:$LINENO: result: $MPICC1" >&5 echo "${ECHO_T}$MPICC1" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi # Extract the first word of "hcc", so it can be a program name with args. set dummy hcc; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_MPICC2+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $MPICC2 in [\\/]* | ?:[\\/]*) ac_cv_path_MPICC2="$MPICC2" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_MPICC2="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi MPICC2=$ac_cv_path_MPICC2 if test -n "$MPICC2"; then echo "$as_me:$LINENO: result: $MPICC2" >&5 echo "${ECHO_T}$MPICC2" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi # Extract the first word of "mpicc", so it can be a program name with args. set dummy mpicc; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_MPICC3+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $MPICC3 in [\\/]* | ?:[\\/]*) ac_cv_path_MPICC3="$MPICC3" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_MPICC3="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi MPICC3=$ac_cv_path_MPICC3 if test -n "$MPICC3"; then echo "$as_me:$LINENO: result: $MPICC3" >&5 echo "${ECHO_T}$MPICC3" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi # Extract the first word of "mpicc_lam", so it can be a program name with args. set dummy mpicc_lam; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_MPICC4+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $MPICC4 in [\\/]* | ?:[\\/]*) ac_cv_path_MPICC4="$MPICC4" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_MPICC4="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi MPICC4=$ac_cv_path_MPICC4 if test -n "$MPICC4"; then echo "$as_me:$LINENO: result: $MPICC4" >&5 echo "${ECHO_T}$MPICC4" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi # Extract the first word of "mpicc_mpich", so it can be a program name with args. set dummy mpicc_mpich; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_MPICC5+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $MPICC5 in [\\/]* | ?:[\\/]*) ac_cv_path_MPICC5="$MPICC5" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_MPICC5="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi MPICC5=$ac_cv_path_MPICC5 if test -n "$MPICC5"; then echo "$as_me:$LINENO: result: $MPICC5" >&5 echo "${ECHO_T}$MPICC5" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi # Extract the first word of "cc", so it can be a program name with args. set dummy cc; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_MPICC6+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $MPICC6 in [\\/]* | ?:[\\/]*) ac_cv_path_MPICC6="$MPICC6" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_MPICC6="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi MPICC6=$ac_cv_path_MPICC6 if test -n "$MPICC6"; then echo "$as_me:$LINENO: result: $MPICC6" >&5 echo "${ECHO_T}$MPICC6" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi if test "$MPICC0" != "" ; then if test "$MPICCSET" = "" ; then cat > conftest.c < int main (int argc, char **argv) { MPI_Init(&argc,&argv); MPI_Finalize(); exit(0); } EOF MPICC=$MPICC0 if test "$MPICC" != "" ; then echo "$as_me:$LINENO: checking whether $MPICC works as MPI compiler" >&5 echo $ECHO_N "checking whether $MPICC works as MPI compiler... $ECHO_C" >&6 $MPICC conftest.c -o conftest > /dev/null 2>&1 if test $? = 0 ; then echo "$as_me:$LINENO: result: yes" >&5 echo "${ECHO_T}yes" >&6 #MPICC=$MPICC MPILIBS= MPICCSET=$MPICC PPUZZLE=ppuzzle else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 echo "$as_me:$LINENO: checking whether $MPICC needs -lmpi" >&5 echo $ECHO_N "checking whether $MPICC needs -lmpi... $ECHO_C" >&6 $MPICC conftest.c -o conftest -lmpi > /dev/null 2>&1 if test $? = 0 ; then echo "$as_me:$LINENO: result: yes" >&5 echo "${ECHO_T}yes" >&6 #MPICC=$PCC MPILIBS=-lmpi MPICCSET=$MPICC PPUZZLE=ppuzzle else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 MPICC= MPILIBS= MPICCSET= PPUZZLE= fi fi fi rm -f *.conftest* fi fi if test "$MPICC1" != "" ; then if test "$MPICCSET" = "" ; then cat > conftest.c < int main (int argc, char **argv) { MPI_Init(&argc,&argv); MPI_Finalize(); exit(0); } EOF MPICC=$MPICC1 if test "$MPICC" != "" ; then echo "$as_me:$LINENO: checking whether $MPICC works as MPI compiler" >&5 echo $ECHO_N "checking whether $MPICC works as MPI compiler... $ECHO_C" >&6 $MPICC conftest.c -o conftest > /dev/null 2>&1 if test $? = 0 ; then echo "$as_me:$LINENO: result: yes" >&5 echo "${ECHO_T}yes" >&6 #MPICC=$MPICC MPILIBS= MPICCSET=$MPICC PPUZZLE=ppuzzle else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 echo "$as_me:$LINENO: checking whether $MPICC needs -lmpi" >&5 echo $ECHO_N "checking whether $MPICC needs -lmpi... $ECHO_C" >&6 $MPICC conftest.c -o conftest -lmpi > /dev/null 2>&1 if test $? = 0 ; then echo "$as_me:$LINENO: result: yes" >&5 echo "${ECHO_T}yes" >&6 #MPICC=$PCC MPILIBS=-lmpi MPICCSET=$MPICC PPUZZLE=ppuzzle else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 MPICC= MPILIBS= MPICCSET= PPUZZLE= fi fi fi rm -f *.conftest* fi fi if test "$MPICC2" != "" ; then if test "$MPICCSET" = "" ; then cat > conftest.c < int main (int argc, char **argv) { MPI_Init(&argc,&argv); MPI_Finalize(); exit(0); } EOF MPICC=$MPICC2 if test "$MPICC" != "" ; then echo "$as_me:$LINENO: checking whether $MPICC works as MPI compiler" >&5 echo $ECHO_N "checking whether $MPICC works as MPI compiler... $ECHO_C" >&6 $MPICC conftest.c -o conftest > /dev/null 2>&1 if test $? = 0 ; then echo "$as_me:$LINENO: result: yes" >&5 echo "${ECHO_T}yes" >&6 #MPICC=$MPICC MPILIBS= MPICCSET=$MPICC PPUZZLE=ppuzzle else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 echo "$as_me:$LINENO: checking whether $MPICC needs -lmpi" >&5 echo $ECHO_N "checking whether $MPICC needs -lmpi... $ECHO_C" >&6 $MPICC conftest.c -o conftest -lmpi > /dev/null 2>&1 if test $? = 0 ; then echo "$as_me:$LINENO: result: yes" >&5 echo "${ECHO_T}yes" >&6 #MPICC=$PCC MPILIBS=-lmpi MPICCSET=$MPICC PPUZZLE=ppuzzle else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 MPICC= MPILIBS= MPICCSET= PPUZZLE= fi fi fi rm -f *.conftest* fi fi if test "$MPICC3" != "" ; then if test "$MPICCSET" = "" ; then cat > conftest.c < int main (int argc, char **argv) { MPI_Init(&argc,&argv); MPI_Finalize(); exit(0); } EOF MPICC=$MPICC3 if test "$MPICC" != "" ; then echo "$as_me:$LINENO: checking whether $MPICC works as MPI compiler" >&5 echo $ECHO_N "checking whether $MPICC works as MPI compiler... $ECHO_C" >&6 $MPICC conftest.c -o conftest > /dev/null 2>&1 if test $? = 0 ; then echo "$as_me:$LINENO: result: yes" >&5 echo "${ECHO_T}yes" >&6 #MPICC=$MPICC MPILIBS= MPICCSET=$MPICC PPUZZLE=ppuzzle else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 echo "$as_me:$LINENO: checking whether $MPICC needs -lmpi" >&5 echo $ECHO_N "checking whether $MPICC needs -lmpi... $ECHO_C" >&6 $MPICC conftest.c -o conftest -lmpi > /dev/null 2>&1 if test $? = 0 ; then echo "$as_me:$LINENO: result: yes" >&5 echo "${ECHO_T}yes" >&6 #MPICC=$PCC MPILIBS=-lmpi MPICCSET=$MPICC PPUZZLE=ppuzzle else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 MPICC= MPILIBS= MPICCSET= PPUZZLE= fi fi fi rm -f *.conftest* fi fi if test "$MPICC4" != "" ; then if test "$MPICCSET" = "" ; then cat > conftest.c < int main (int argc, char **argv) { MPI_Init(&argc,&argv); MPI_Finalize(); exit(0); } EOF MPICC=$MPICC4 if test "$MPICC" != "" ; then echo "$as_me:$LINENO: checking whether $MPICC works as MPI compiler" >&5 echo $ECHO_N "checking whether $MPICC works as MPI compiler... $ECHO_C" >&6 $MPICC conftest.c -o conftest > /dev/null 2>&1 if test $? = 0 ; then echo "$as_me:$LINENO: result: yes" >&5 echo "${ECHO_T}yes" >&6 #MPICC=$MPICC MPILIBS= MPICCSET=$MPICC PPUZZLE=ppuzzle else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 echo "$as_me:$LINENO: checking whether $MPICC needs -lmpi" >&5 echo $ECHO_N "checking whether $MPICC needs -lmpi... $ECHO_C" >&6 $MPICC conftest.c -o conftest -lmpi > /dev/null 2>&1 if test $? = 0 ; then echo "$as_me:$LINENO: result: yes" >&5 echo "${ECHO_T}yes" >&6 #MPICC=$PCC MPILIBS=-lmpi MPICCSET=$MPICC PPUZZLE=ppuzzle else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 MPICC= MPILIBS= MPICCSET= PPUZZLE= fi fi fi rm -f *.conftest* fi fi if test "$MPICC5" != "" ; then if test "$MPICCSET" = "" ; then cat > conftest.c < int main (int argc, char **argv) { MPI_Init(&argc,&argv); MPI_Finalize(); exit(0); } EOF MPICC=$MPICC5 if test "$MPICC" != "" ; then echo "$as_me:$LINENO: checking whether $MPICC works as MPI compiler" >&5 echo $ECHO_N "checking whether $MPICC works as MPI compiler... $ECHO_C" >&6 $MPICC conftest.c -o conftest > /dev/null 2>&1 if test $? = 0 ; then echo "$as_me:$LINENO: result: yes" >&5 echo "${ECHO_T}yes" >&6 #MPICC=$MPICC MPILIBS= MPICCSET=$MPICC PPUZZLE=ppuzzle else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 echo "$as_me:$LINENO: checking whether $MPICC needs -lmpi" >&5 echo $ECHO_N "checking whether $MPICC needs -lmpi... $ECHO_C" >&6 $MPICC conftest.c -o conftest -lmpi > /dev/null 2>&1 if test $? = 0 ; then echo "$as_me:$LINENO: result: yes" >&5 echo "${ECHO_T}yes" >&6 #MPICC=$PCC MPILIBS=-lmpi MPICCSET=$MPICC PPUZZLE=ppuzzle else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 MPICC= MPILIBS= MPICCSET= PPUZZLE= fi fi fi rm -f *.conftest* fi fi if test "$MPICC6" != "" ; then if test "$MPICCSET" = "" ; then cat > conftest.c < int main (int argc, char **argv) { MPI_Init(&argc,&argv); MPI_Finalize(); exit(0); } EOF MPICC=$MPICC6 if test "$MPICC" != "" ; then echo "$as_me:$LINENO: checking whether $MPICC works as MPI compiler" >&5 echo $ECHO_N "checking whether $MPICC works as MPI compiler... $ECHO_C" >&6 $MPICC conftest.c -o conftest > /dev/null 2>&1 if test $? = 0 ; then echo "$as_me:$LINENO: result: yes" >&5 echo "${ECHO_T}yes" >&6 #MPICC=$MPICC MPILIBS= MPICCSET=$MPICC PPUZZLE=ppuzzle else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 echo "$as_me:$LINENO: checking whether $MPICC needs -lmpi" >&5 echo $ECHO_N "checking whether $MPICC needs -lmpi... $ECHO_C" >&6 $MPICC conftest.c -o conftest -lmpi > /dev/null 2>&1 if test $? = 0 ; then echo "$as_me:$LINENO: result: yes" >&5 echo "${ECHO_T}yes" >&6 #MPICC=$PCC MPILIBS=-lmpi MPICCSET=$MPICC PPUZZLE=ppuzzle else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 MPICC= MPILIBS= MPICCSET= PPUZZLE= fi fi fi rm -f *.conftest* fi fi ac_cv_prog_MPICC=$MPICC if test "$MPICC" != "" ; then cat > conftest.c < int main (int argc, char **argv) { printf ("%s-%s", PACKAGE, VERSION); exit(0); } EOF CCQ=$MPICC if test "$CCQ" != "" ; then echo "$as_me:$LINENO: checking whether $CCQ handles quotes correctly" >&5 echo $ECHO_N "checking whether $CCQ handles quotes correctly... $ECHO_C" >&6 $CCQ -DPACKAGE=\"$PACKAGE\" -DVERSION=\"$VERSION\" conftest.c -o conftest > /dev/null 2>&1 if test $? = 0 ; then DUMMY=`./conftest` if test "$DUMMY" = "$PACKAGE-$VERSION" ; then echo "$as_me:$LINENO: result: yes" >&5 echo "${ECHO_T}yes" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi fi mv conftest.c `basename $CCQ`.conftest.c rm -f *.conftest* fi if test "$CC" != "" ; then cat > conftest.c < int main (int argc, char **argv) { printf ("%s-%s", PACKAGE, VERSION); exit(0); } EOF CCQ=$CC if test "$CCQ" != "" ; then echo "$as_me:$LINENO: checking whether $CCQ handles quotes correctly" >&5 echo $ECHO_N "checking whether $CCQ handles quotes correctly... $ECHO_C" >&6 $CCQ -DPACKAGE=\"$PACKAGE\" -DVERSION=\"$VERSION\" conftest.c -o conftest > /dev/null 2>&1 if test $? = 0 ; then DUMMY=`./conftest` if test "$DUMMY" = "$PACKAGE-$VERSION" ; then echo "$as_me:$LINENO: result: yes" >&5 echo "${ECHO_T}yes" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi fi mv conftest.c `basename $CCQ`.conftest.c rm -f *.conftest* fi echo "$as_me:$LINENO: checking for main in -lm" >&5 echo $ECHO_N "checking for main in -lm... $ECHO_C" >&6 if test "${ac_cv_lib_m_main+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lm $LIBS" cat >conftest.$ac_ext <<_ACEOF #line $LINENO "configure" #include "confdefs.h" #ifdef F77_DUMMY_MAIN # ifdef __cplusplus extern "C" # endif int F77_DUMMY_MAIN() { return 1; } #endif int main () { main (); ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -s conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then ac_cv_lib_m_main=yes else echo "$as_me: failed program was:" >&5 cat conftest.$ac_ext >&5 ac_cv_lib_m_main=no fi rm -f conftest.$ac_objext conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi echo "$as_me:$LINENO: result: $ac_cv_lib_m_main" >&5 echo "${ECHO_T}$ac_cv_lib_m_main" >&6 if test $ac_cv_lib_m_main = yes; then cat >>confdefs.h <<_ACEOF #define HAVE_LIBM 1 _ACEOF LIBS="-lm $LIBS" fi ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu echo "$as_me:$LINENO: checking how to run the C preprocessor" >&5 echo $ECHO_N "checking how to run the C preprocessor... $ECHO_C" >&6 # On Suns, sometimes $CPP names a directory. if test -n "$CPP" && test -d "$CPP"; then CPP= fi if test -z "$CPP"; then if test "${ac_cv_prog_CPP+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else # Double quotes because CPP needs to be expanded for CPP in "$CC -E" "$CC -E -traditional-cpp" "/lib/cpp" do ac_preproc_ok=false for ac_c_preproc_warn_flag in '' yes do # Use a header file that comes with gcc, so configuring glibc # with a fresh cross-compiler works. # On the NeXT, cc -E runs the code through the compiler's parser, # not just through cpp. "Syntax error" is here to catch this case. cat >conftest.$ac_ext <<_ACEOF #line $LINENO "configure" #include "confdefs.h" #include Syntax error _ACEOF if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 ac_status=$? egrep -v '^ *\+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } >/dev/null; then if test -s conftest.err; then ac_cpp_err=$ac_c_preproc_warn_flag else ac_cpp_err= fi else ac_cpp_err=yes fi if test -z "$ac_cpp_err"; then : else echo "$as_me: failed program was:" >&5 cat conftest.$ac_ext >&5 # Broken: fails on valid input. continue fi rm -f conftest.err conftest.$ac_ext # OK, works on sane cases. Now check whether non-existent headers # can be detected and how. cat >conftest.$ac_ext <<_ACEOF #line $LINENO "configure" #include "confdefs.h" #include _ACEOF if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 ac_status=$? egrep -v '^ *\+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } >/dev/null; then if test -s conftest.err; then ac_cpp_err=$ac_c_preproc_warn_flag else ac_cpp_err= fi else ac_cpp_err=yes fi if test -z "$ac_cpp_err"; then # Broken: success on invalid input. continue else echo "$as_me: failed program was:" >&5 cat conftest.$ac_ext >&5 # Passes both tests. ac_preproc_ok=: break fi rm -f conftest.err conftest.$ac_ext done # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. rm -f conftest.err conftest.$ac_ext if $ac_preproc_ok; then break fi done ac_cv_prog_CPP=$CPP fi CPP=$ac_cv_prog_CPP else ac_cv_prog_CPP=$CPP fi echo "$as_me:$LINENO: result: $CPP" >&5 echo "${ECHO_T}$CPP" >&6 ac_preproc_ok=false for ac_c_preproc_warn_flag in '' yes do # Use a header file that comes with gcc, so configuring glibc # with a fresh cross-compiler works. # On the NeXT, cc -E runs the code through the compiler's parser, # not just through cpp. "Syntax error" is here to catch this case. cat >conftest.$ac_ext <<_ACEOF #line $LINENO "configure" #include "confdefs.h" #include Syntax error _ACEOF if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 ac_status=$? egrep -v '^ *\+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } >/dev/null; then if test -s conftest.err; then ac_cpp_err=$ac_c_preproc_warn_flag else ac_cpp_err= fi else ac_cpp_err=yes fi if test -z "$ac_cpp_err"; then : else echo "$as_me: failed program was:" >&5 cat conftest.$ac_ext >&5 # Broken: fails on valid input. continue fi rm -f conftest.err conftest.$ac_ext # OK, works on sane cases. Now check whether non-existent headers # can be detected and how. cat >conftest.$ac_ext <<_ACEOF #line $LINENO "configure" #include "confdefs.h" #include _ACEOF if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 ac_status=$? egrep -v '^ *\+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } >/dev/null; then if test -s conftest.err; then ac_cpp_err=$ac_c_preproc_warn_flag else ac_cpp_err= fi else ac_cpp_err=yes fi if test -z "$ac_cpp_err"; then # Broken: success on invalid input. continue else echo "$as_me: failed program was:" >&5 cat conftest.$ac_ext >&5 # Passes both tests. ac_preproc_ok=: break fi rm -f conftest.err conftest.$ac_ext done # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. rm -f conftest.err conftest.$ac_ext if $ac_preproc_ok; then : else { { echo "$as_me:$LINENO: error: C preprocessor \"$CPP\" fails sanity check" >&5 echo "$as_me: error: C preprocessor \"$CPP\" fails sanity check" >&2;} { (exit 1); exit 1; }; } fi ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu echo "$as_me:$LINENO: checking for ANSI C header files" >&5 echo $ECHO_N "checking for ANSI C header files... $ECHO_C" >&6 if test "${ac_cv_header_stdc+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else cat >conftest.$ac_ext <<_ACEOF #line $LINENO "configure" #include "confdefs.h" #include #include #include #include _ACEOF if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 ac_status=$? egrep -v '^ *\+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } >/dev/null; then if test -s conftest.err; then ac_cpp_err=$ac_c_preproc_warn_flag else ac_cpp_err= fi else ac_cpp_err=yes fi if test -z "$ac_cpp_err"; then ac_cv_header_stdc=yes else echo "$as_me: failed program was:" >&5 cat conftest.$ac_ext >&5 ac_cv_header_stdc=no fi rm -f conftest.err conftest.$ac_ext if test $ac_cv_header_stdc = yes; then # SunOS 4.x string.h does not declare mem*, contrary to ANSI. cat >conftest.$ac_ext <<_ACEOF #line $LINENO "configure" #include "confdefs.h" #include _ACEOF if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | egrep "memchr" >/dev/null 2>&1; then : else ac_cv_header_stdc=no fi rm -f conftest* fi if test $ac_cv_header_stdc = yes; then # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI. cat >conftest.$ac_ext <<_ACEOF #line $LINENO "configure" #include "confdefs.h" #include _ACEOF if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | egrep "free" >/dev/null 2>&1; then : else ac_cv_header_stdc=no fi rm -f conftest* fi if test $ac_cv_header_stdc = yes; then # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi. if test "$cross_compiling" = yes; then : else cat >conftest.$ac_ext <<_ACEOF #line $LINENO "configure" #include "confdefs.h" #include #if ((' ' & 0x0FF) == 0x020) # define ISLOWER(c) ('a' <= (c) && (c) <= 'z') # define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c)) #else # define ISLOWER(c) (('a' <= (c) && (c) <= 'i') \ || ('j' <= (c) && (c) <= 'r') \ || ('s' <= (c) && (c) <= 'z')) # define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c)) #endif #define XOR(e, f) (((e) && !(f)) || (!(e) && (f))) int main () { int i; for (i = 0; i < 256; i++) if (XOR (islower (i), ISLOWER (i)) || toupper (i) != TOUPPER (i)) exit(2); exit (0); } _ACEOF rm -f conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='./conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then : else echo "$as_me: program exited with status $ac_status" >&5 echo "$as_me: failed program was:" >&5 cat conftest.$ac_ext >&5 ( exit $ac_status ) ac_cv_header_stdc=no fi rm -f core core.* *.core conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext fi fi fi echo "$as_me:$LINENO: result: $ac_cv_header_stdc" >&5 echo "${ECHO_T}$ac_cv_header_stdc" >&6 if test $ac_cv_header_stdc = yes; then cat >>confdefs.h <<\_ACEOF #define STDC_HEADERS 1 _ACEOF fi # On IRIX 5.3, sys/types and inttypes.h are conflicting. for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \ inttypes.h stdint.h unistd.h do as_ac_Header=`echo "ac_cv_header_$ac_header" | $as_tr_sh` echo "$as_me:$LINENO: checking for $ac_header" >&5 echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6 if eval "test \"\${$as_ac_Header+set}\" = set"; then echo $ECHO_N "(cached) $ECHO_C" >&6 else cat >conftest.$ac_ext <<_ACEOF #line $LINENO "configure" #include "confdefs.h" $ac_includes_default #include <$ac_header> _ACEOF rm -f conftest.$ac_objext if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 (eval $ac_compile) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -s conftest.$ac_objext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then eval "$as_ac_Header=yes" else echo "$as_me: failed program was:" >&5 cat conftest.$ac_ext >&5 eval "$as_ac_Header=no" fi rm -f conftest.$ac_objext conftest.$ac_ext fi echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Header'}'`" >&5 echo "${ECHO_T}`eval echo '${'$as_ac_Header'}'`" >&6 if test `eval echo '${'$as_ac_Header'}'` = yes; then cat >>confdefs.h <<_ACEOF #define `echo "HAVE_$ac_header" | $as_tr_cpp` 1 _ACEOF fi done for ac_header in limits.h do as_ac_Header=`echo "ac_cv_header_$ac_header" | $as_tr_sh` if eval "test \"\${$as_ac_Header+set}\" = set"; then echo "$as_me:$LINENO: checking for $ac_header" >&5 echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6 if eval "test \"\${$as_ac_Header+set}\" = set"; then echo $ECHO_N "(cached) $ECHO_C" >&6 fi echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Header'}'`" >&5 echo "${ECHO_T}`eval echo '${'$as_ac_Header'}'`" >&6 else # Is the header compilable? echo "$as_me:$LINENO: checking $ac_header usability" >&5 echo $ECHO_N "checking $ac_header usability... $ECHO_C" >&6 cat >conftest.$ac_ext <<_ACEOF #line $LINENO "configure" #include "confdefs.h" $ac_includes_default #include <$ac_header> _ACEOF rm -f conftest.$ac_objext if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 (eval $ac_compile) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -s conftest.$ac_objext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then ac_header_compiler=yes else echo "$as_me: failed program was:" >&5 cat conftest.$ac_ext >&5 ac_header_compiler=no fi rm -f conftest.$ac_objext conftest.$ac_ext echo "$as_me:$LINENO: result: $ac_header_compiler" >&5 echo "${ECHO_T}$ac_header_compiler" >&6 # Is the header present? echo "$as_me:$LINENO: checking $ac_header presence" >&5 echo $ECHO_N "checking $ac_header presence... $ECHO_C" >&6 cat >conftest.$ac_ext <<_ACEOF #line $LINENO "configure" #include "confdefs.h" #include <$ac_header> _ACEOF if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 ac_status=$? egrep -v '^ *\+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } >/dev/null; then if test -s conftest.err; then ac_cpp_err=$ac_c_preproc_warn_flag else ac_cpp_err= fi else ac_cpp_err=yes fi if test -z "$ac_cpp_err"; then ac_header_preproc=yes else echo "$as_me: failed program was:" >&5 cat conftest.$ac_ext >&5 ac_header_preproc=no fi rm -f conftest.err conftest.$ac_ext echo "$as_me:$LINENO: result: $ac_header_preproc" >&5 echo "${ECHO_T}$ac_header_preproc" >&6 # So? What about this header? case $ac_header_compiler:$ac_header_preproc in yes:no ) { echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5 echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;} { echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5 echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;};; no:yes ) { echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5 echo "$as_me: WARNING: $ac_header: present but cannot be compiled" >&2;} { echo "$as_me:$LINENO: WARNING: $ac_header: check for missing prerequisite headers?" >&5 echo "$as_me: WARNING: $ac_header: check for missing prerequisite headers?" >&2;} { echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5 echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;};; esac echo "$as_me:$LINENO: checking for $ac_header" >&5 echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6 if eval "test \"\${$as_ac_Header+set}\" = set"; then echo $ECHO_N "(cached) $ECHO_C" >&6 else eval "$as_ac_Header=$ac_header_preproc" fi echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Header'}'`" >&5 echo "${ECHO_T}`eval echo '${'$as_ac_Header'}'`" >&6 fi if test `eval echo '${'$as_ac_Header'}'` = yes; then cat >>confdefs.h <<_ACEOF #define `echo "HAVE_$ac_header" | $as_tr_cpp` 1 _ACEOF fi done echo "$as_me:$LINENO: checking for $CC option to accept ANSI C" >&5 echo $ECHO_N "checking for $CC option to accept ANSI C... $ECHO_C" >&6 if test "${ac_cv_prog_cc_stdc+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else ac_cv_prog_cc_stdc=no ac_save_CC=$CC cat >conftest.$ac_ext <<_ACEOF #line $LINENO "configure" #include "confdefs.h" #include #include #include #include /* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */ struct buf { int x; }; FILE * (*rcsopen) (struct buf *, struct stat *, int); static char *e (p, i) char **p; int i; { return p[i]; } static char *f (char * (*g) (char **, int), char **p, ...) { char *s; va_list v; va_start (v,p); s = g (p, va_arg (v,int)); va_end (v); return s; } int test (int i, double x); struct s1 {int (*f) (int a);}; struct s2 {int (*f) (double a);}; int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int); int argc; char **argv; #ifdef F77_DUMMY_MAIN # ifdef __cplusplus extern "C" # endif int F77_DUMMY_MAIN() { return 1; } #endif int main () { return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1]; ; return 0; } _ACEOF # Don't try gcc -ansi; that turns off useful extensions and # breaks some systems' header files. # AIX -qlanglvl=ansi # Ultrix and OSF/1 -std1 # HP-UX 10.20 and later -Ae # HP-UX older versions -Aa -D_HPUX_SOURCE # SVR4 -Xc -D__EXTENSIONS__ for ac_arg in "" -qlanglvl=ansi -std1 -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" do CC="$ac_save_CC $ac_arg" rm -f conftest.$ac_objext if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 (eval $ac_compile) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -s conftest.$ac_objext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then ac_cv_prog_cc_stdc=$ac_arg break else echo "$as_me: failed program was:" >&5 cat conftest.$ac_ext >&5 fi rm -f conftest.$ac_objext done rm -f conftest.$ac_ext conftest.$ac_objext CC=$ac_save_CC fi case "x$ac_cv_prog_cc_stdc" in x|xno) echo "$as_me:$LINENO: result: none needed" >&5 echo "${ECHO_T}none needed" >&6 ;; *) echo "$as_me:$LINENO: result: $ac_cv_prog_cc_stdc" >&5 echo "${ECHO_T}$ac_cv_prog_cc_stdc" >&6 CC="$CC $ac_cv_prog_cc_stdc" ;; esac echo "$as_me:$LINENO: checking for an ANSI C-conforming const" >&5 echo $ECHO_N "checking for an ANSI C-conforming const... $ECHO_C" >&6 if test "${ac_cv_c_const+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else cat >conftest.$ac_ext <<_ACEOF #line $LINENO "configure" #include "confdefs.h" #ifdef F77_DUMMY_MAIN # ifdef __cplusplus extern "C" # endif int F77_DUMMY_MAIN() { return 1; } #endif int main () { /* FIXME: Include the comments suggested by Paul. */ #ifndef __cplusplus /* Ultrix mips cc rejects this. */ typedef int charset[2]; const charset x; /* SunOS 4.1.1 cc rejects this. */ char const *const *ccp; char **p; /* NEC SVR4.0.2 mips cc rejects this. */ struct point {int x, y;}; static struct point const zero = {0,0}; /* AIX XL C 1.02.0.0 rejects this. It does not let you subtract one const X* pointer from another in an arm of an if-expression whose if-part is not a constant expression */ const char *g = "string"; ccp = &g + (g ? g-g : 0); /* HPUX 7.0 cc rejects these. */ ++ccp; p = (char**) ccp; ccp = (char const *const *) p; { /* SCO 3.2v4 cc rejects this. */ char *t; char const *s = 0 ? 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See the GNU # General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. # # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that program. # Written by Per Bothner . # Please send patches to . # # This script attempts to guess a canonical system name similar to # config.sub. If it succeeds, it prints the system name on stdout, and # exits with 0. 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The machine name # can be virtually everything (everything which is not # "atarist" or "atariste" at least should have a processor # > m68000). The system name ranges from "MiNT" over "FreeMiNT" # to the lowercase version "mint" (or "freemint"). Finally # the system name "TOS" denotes a system which is actually not # MiNT. But MiNT is downward compatible to TOS, so this should # be no problem. atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit 0 ;; atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit 0 ;; *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit 0 ;; milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*) echo m68k-milan-mint${UNAME_RELEASE} exit 0 ;; hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*) echo m68k-hades-mint${UNAME_RELEASE} exit 0 ;; *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*) echo m68k-unknown-mint${UNAME_RELEASE} exit 0 ;; sun3*:OpenBSD:*:*) echo m68k-unknown-openbsd${UNAME_RELEASE} exit 0 ;; mac68k:OpenBSD:*:*) echo m68k-unknown-openbsd${UNAME_RELEASE} exit 0 ;; mvme68k:OpenBSD:*:*) echo m68k-unknown-openbsd${UNAME_RELEASE} exit 0 ;; mvme88k:OpenBSD:*:*) echo m88k-unknown-openbsd${UNAME_RELEASE} exit 0 ;; powerpc:machten:*:*) echo powerpc-apple-machten${UNAME_RELEASE} exit 0 ;; RISC*:Mach:*:*) echo mips-dec-mach_bsd4.3 exit 0 ;; RISC*:ULTRIX:*:*) echo mips-dec-ultrix${UNAME_RELEASE} exit 0 ;; VAX*:ULTRIX*:*:*) echo vax-dec-ultrix${UNAME_RELEASE} exit 0 ;; 2020:CLIX:*:* | 2430:CLIX:*:*) echo clipper-intergraph-clix${UNAME_RELEASE} exit 0 ;; mips:*:*:UMIPS | mips:*:*:RISCos) sed 's/^ //' << EOF >$dummy.c #ifdef __cplusplus #include /* for printf() prototype */ int main (int argc, char *argv[]) { #else int main (argc, argv) int argc; char *argv[]; { #endif #if defined (host_mips) && defined (MIPSEB) #if defined (SYSTYPE_SYSV) printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0); #endif #if defined (SYSTYPE_SVR4) printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0); #endif #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD) printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0); #endif #endif exit (-1); } EOF eval $set_cc_for_build $CC_FOR_BUILD $dummy.c -o $dummy \ && ./$dummy `echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` \ && rm -f $dummy.c $dummy && exit 0 rm -f $dummy.c $dummy echo mips-mips-riscos${UNAME_RELEASE} exit 0 ;; Motorola:PowerMAX_OS:*:*) echo powerpc-motorola-powermax exit 0 ;; Night_Hawk:Power_UNIX:*:*) echo powerpc-harris-powerunix exit 0 ;; m88k:CX/UX:7*:*) echo m88k-harris-cxux7 exit 0 ;; m88k:*:4*:R4*) echo m88k-motorola-sysv4 exit 0 ;; m88k:*:3*:R3*) echo m88k-motorola-sysv3 exit 0 ;; AViiON:dgux:*:*) # DG/UX returns AViiON for all architectures UNAME_PROCESSOR=`/usr/bin/uname -p` if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ] then if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \ [ ${TARGET_BINARY_INTERFACE}x = x ] then echo m88k-dg-dgux${UNAME_RELEASE} else echo m88k-dg-dguxbcs${UNAME_RELEASE} fi else echo i586-dg-dgux${UNAME_RELEASE} fi exit 0 ;; M88*:DolphinOS:*:*) # DolphinOS (SVR3) echo m88k-dolphin-sysv3 exit 0 ;; M88*:*:R3*:*) # Delta 88k system running SVR3 echo m88k-motorola-sysv3 exit 0 ;; XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3) echo m88k-tektronix-sysv3 exit 0 ;; Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD) echo m68k-tektronix-bsd exit 0 ;; *:IRIX*:*:*) echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'` exit 0 ;; ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX. echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id exit 0 ;; # Note that: echo "'`uname -s`'" gives 'AIX ' i*86:AIX:*:*) echo i386-ibm-aix exit 0 ;; ia64:AIX:*:*) if [ -x /usr/bin/oslevel ] ; then IBM_REV=`/usr/bin/oslevel` else IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} fi echo ${UNAME_MACHINE}-ibm-aix${IBM_REV} exit 0 ;; *:AIX:2:3) if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then sed 's/^ //' << EOF >$dummy.c #include main() { if (!__power_pc()) exit(1); puts("powerpc-ibm-aix3.2.5"); exit(0); } EOF eval $set_cc_for_build $CC_FOR_BUILD $dummy.c -o $dummy && ./$dummy && rm -f $dummy.c $dummy && exit 0 rm -f $dummy.c $dummy echo rs6000-ibm-aix3.2.5 elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then echo rs6000-ibm-aix3.2.4 else echo rs6000-ibm-aix3.2 fi exit 0 ;; *:AIX:*:[45]) IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | head -1 | awk '{ print $1 }'` if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then IBM_ARCH=rs6000 else IBM_ARCH=powerpc fi if [ -x /usr/bin/oslevel ] ; then IBM_REV=`/usr/bin/oslevel` else IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} fi echo ${IBM_ARCH}-ibm-aix${IBM_REV} exit 0 ;; *:AIX:*:*) echo rs6000-ibm-aix exit 0 ;; ibmrt:4.4BSD:*|romp-ibm:BSD:*) echo romp-ibm-bsd4.4 exit 0 ;; ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and echo romp-ibm-bsd${UNAME_RELEASE} # 4.3 with uname added to exit 0 ;; # report: romp-ibm BSD 4.3 *:BOSX:*:*) echo rs6000-bull-bosx exit 0 ;; DPX/2?00:B.O.S.:*:*) echo m68k-bull-sysv3 exit 0 ;; 9000/[34]??:4.3bsd:1.*:*) echo m68k-hp-bsd exit 0 ;; hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*) echo m68k-hp-bsd4.4 exit 0 ;; 9000/[34678]??:HP-UX:*:*) HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` case "${UNAME_MACHINE}" in 9000/31? ) HP_ARCH=m68000 ;; 9000/[34]?? ) HP_ARCH=m68k ;; 9000/[678][0-9][0-9]) case "${HPUX_REV}" in 11.[0-9][0-9]) if [ -x /usr/bin/getconf ]; then sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null` sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null` case "${sc_cpu_version}" in 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1 532) # CPU_PA_RISC2_0 case "${sc_kernel_bits}" in 32) HP_ARCH="hppa2.0n" ;; 64) HP_ARCH="hppa2.0w" ;; esac ;; esac fi ;; esac if [ "${HP_ARCH}" = "" ]; then sed 's/^ //' << EOF >$dummy.c #define _HPUX_SOURCE #include #include int main () { #if defined(_SC_KERNEL_BITS) long bits = sysconf(_SC_KERNEL_BITS); #endif long cpu = sysconf (_SC_CPU_VERSION); switch (cpu) { case CPU_PA_RISC1_0: puts ("hppa1.0"); break; case CPU_PA_RISC1_1: puts ("hppa1.1"); break; case CPU_PA_RISC2_0: #if defined(_SC_KERNEL_BITS) switch (bits) { case 64: puts ("hppa2.0w"); break; case 32: puts ("hppa2.0n"); break; default: puts ("hppa2.0"); break; } break; #else /* !defined(_SC_KERNEL_BITS) */ puts ("hppa2.0"); break; #endif default: puts ("hppa1.0"); break; } exit (0); } EOF eval $set_cc_for_build (CCOPTS= $CC_FOR_BUILD $dummy.c -o $dummy 2>/dev/null ) && HP_ARCH=`./$dummy` if test -z "$HP_ARCH"; then HP_ARCH=hppa; fi rm -f $dummy.c $dummy fi ;; esac echo ${HP_ARCH}-hp-hpux${HPUX_REV} exit 0 ;; ia64:HP-UX:*:*) HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` echo ia64-hp-hpux${HPUX_REV} exit 0 ;; 3050*:HI-UX:*:*) sed 's/^ //' << EOF >$dummy.c #include int main () { long cpu = sysconf (_SC_CPU_VERSION); /* The order matters, because CPU_IS_HP_MC68K erroneously returns true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct results, however. */ if (CPU_IS_PA_RISC (cpu)) { switch (cpu) { case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break; case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break; case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break; default: puts ("hppa-hitachi-hiuxwe2"); break; } } else if (CPU_IS_HP_MC68K (cpu)) puts ("m68k-hitachi-hiuxwe2"); else puts ("unknown-hitachi-hiuxwe2"); exit (0); } EOF eval $set_cc_for_build $CC_FOR_BUILD $dummy.c -o $dummy && ./$dummy && rm -f $dummy.c $dummy && exit 0 rm -f $dummy.c $dummy echo unknown-hitachi-hiuxwe2 exit 0 ;; 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* ) echo hppa1.1-hp-bsd exit 0 ;; 9000/8??:4.3bsd:*:*) echo hppa1.0-hp-bsd exit 0 ;; *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*) echo hppa1.0-hp-mpeix exit 0 ;; hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* ) echo hppa1.1-hp-osf exit 0 ;; hp8??:OSF1:*:*) echo hppa1.0-hp-osf exit 0 ;; i*86:OSF1:*:*) if [ -x /usr/sbin/sysversion ] ; then echo ${UNAME_MACHINE}-unknown-osf1mk else echo ${UNAME_MACHINE}-unknown-osf1 fi exit 0 ;; parisc*:Lites*:*:*) echo hppa1.1-hp-lites exit 0 ;; hppa*:OpenBSD:*:*) echo hppa-unknown-openbsd exit 0 ;; C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*) echo c1-convex-bsd exit 0 ;; C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*) if getsysinfo -f scalar_acc then echo c32-convex-bsd else echo c2-convex-bsd fi exit 0 ;; C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*) echo c34-convex-bsd exit 0 ;; C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*) echo c38-convex-bsd exit 0 ;; C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*) echo c4-convex-bsd exit 0 ;; CRAY*X-MP:*:*:*) echo xmp-cray-unicos exit 0 ;; CRAY*Y-MP:*:*:*) echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit 0 ;; CRAY*[A-Z]90:*:*:*) echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \ | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \ -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \ -e 's/\.[^.]*$/.X/' exit 0 ;; CRAY*TS:*:*:*) echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit 0 ;; CRAY*T3D:*:*:*) echo alpha-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit 0 ;; CRAY*T3E:*:*:*) echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit 0 ;; CRAY*SV1:*:*:*) echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit 0 ;; CRAY-2:*:*:*) echo cray2-cray-unicos exit 0 ;; F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*) FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'` echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" exit 0 ;; hp300:OpenBSD:*:*) echo m68k-unknown-openbsd${UNAME_RELEASE} exit 0 ;; i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*) echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE} exit 0 ;; sparc*:BSD/OS:*:*) echo sparc-unknown-bsdi${UNAME_RELEASE} exit 0 ;; *:BSD/OS:*:*) echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE} exit 0 ;; *:FreeBSD:*:*) echo ${UNAME_MACHINE}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` exit 0 ;; *:OpenBSD:*:*) echo ${UNAME_MACHINE}-unknown-openbsd`echo ${UNAME_RELEASE}|sed -e 's/[-_].*/\./'` exit 0 ;; i*:CYGWIN*:*) echo ${UNAME_MACHINE}-pc-cygwin exit 0 ;; i*:MINGW*:*) echo ${UNAME_MACHINE}-pc-mingw32 exit 0 ;; i*:PW*:*) echo ${UNAME_MACHINE}-pc-pw32 exit 0 ;; i*:Windows_NT*:* | Pentium*:Windows_NT*:*) # How do we know it's Interix rather than the generic POSIX subsystem? # It also conflicts with pre-2.0 versions of AT&T UWIN. Should we # UNAME_MACHINE based on the output of uname instead of i386? echo i386-pc-interix exit 0 ;; i*:UWIN*:*) echo ${UNAME_MACHINE}-pc-uwin exit 0 ;; p*:CYGWIN*:*) echo powerpcle-unknown-cygwin exit 0 ;; prep*:SunOS:5.*:*) echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit 0 ;; *:GNU:*:*) echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'` exit 0 ;; i*86:Minix:*:*) echo ${UNAME_MACHINE}-pc-minix exit 0 ;; arm*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit 0 ;; ia64:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux exit 0 ;; m68*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit 0 ;; mips:Linux:*:*) case `sed -n '/^byte/s/^.*: \(.*\) endian/\1/p' < /proc/cpuinfo` in big) echo mips-unknown-linux-gnu && exit 0 ;; little) echo mipsel-unknown-linux-gnu && exit 0 ;; esac ;; ppc:Linux:*:*) echo powerpc-unknown-linux-gnu exit 0 ;; ppc64:Linux:*:*) echo powerpc64-unknown-linux-gnu exit 0 ;; alpha:Linux:*:*) case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in EV5) UNAME_MACHINE=alphaev5 ;; EV56) UNAME_MACHINE=alphaev56 ;; PCA56) UNAME_MACHINE=alphapca56 ;; PCA57) UNAME_MACHINE=alphapca56 ;; EV6) UNAME_MACHINE=alphaev6 ;; EV67) UNAME_MACHINE=alphaev67 ;; EV68*) UNAME_MACHINE=alphaev68 ;; esac objdump --private-headers /bin/sh | grep ld.so.1 >/dev/null if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC} exit 0 ;; parisc:Linux:*:* | hppa:Linux:*:*) # Look for CPU level case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in PA7*) echo hppa1.1-unknown-linux-gnu ;; PA8*) echo hppa2.0-unknown-linux-gnu ;; *) echo hppa-unknown-linux-gnu ;; esac exit 0 ;; parisc64:Linux:*:* | hppa64:Linux:*:*) echo hppa64-unknown-linux-gnu exit 0 ;; s390:Linux:*:* | s390x:Linux:*:*) echo ${UNAME_MACHINE}-ibm-linux exit 0 ;; sh*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit 0 ;; sparc:Linux:*:* | sparc64:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit 0 ;; x86_64:Linux:*:*) echo x86_64-unknown-linux-gnu exit 0 ;; i*86:Linux:*:*) # The BFD linker knows what the default object file format is, so # first see if it will tell us. cd to the root directory to prevent # problems with other programs or directories called `ld' in the path. ld_supported_targets=`cd /; ld --help 2>&1 \ | sed -ne '/supported targets:/!d s/[ ][ ]*/ /g s/.*supported targets: *// s/ .*// p'` case "$ld_supported_targets" in elf32-i386) TENTATIVE="${UNAME_MACHINE}-pc-linux-gnu" ;; a.out-i386-linux) echo "${UNAME_MACHINE}-pc-linux-gnuaout" exit 0 ;; coff-i386) echo "${UNAME_MACHINE}-pc-linux-gnucoff" exit 0 ;; "") # Either a pre-BFD a.out linker (linux-gnuoldld) or # one that does not give us useful --help. echo "${UNAME_MACHINE}-pc-linux-gnuoldld" exit 0 ;; esac # Determine whether the default compiler is a.out or elf cat >$dummy.c < #ifdef __cplusplus #include /* for printf() prototype */ int main (int argc, char *argv[]) { #else int main (argc, argv) int argc; char *argv[]; { #endif #ifdef __ELF__ # ifdef __GLIBC__ # if __GLIBC__ >= 2 printf ("%s-pc-linux-gnu\n", argv[1]); # else printf ("%s-pc-linux-gnulibc1\n", argv[1]); # endif # else printf ("%s-pc-linux-gnulibc1\n", argv[1]); # endif #else printf ("%s-pc-linux-gnuaout\n", argv[1]); #endif return 0; } EOF eval $set_cc_for_build $CC_FOR_BUILD $dummy.c -o $dummy 2>/dev/null && ./$dummy "${UNAME_MACHINE}" && rm -f $dummy.c $dummy && exit 0 rm -f $dummy.c $dummy test x"${TENTATIVE}" != x && echo "${TENTATIVE}" && exit 0 ;; i*86:DYNIX/ptx:4*:*) # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there. # earlier versions are messed up and put the nodename in both # sysname and nodename. echo i386-sequent-sysv4 exit 0 ;; i*86:UNIX_SV:4.2MP:2.*) # Unixware is an offshoot of SVR4, but it has its own version # number series starting with 2... # I am not positive that other SVR4 systems won't match this, # I just have to hope. -- rms. # Use sysv4.2uw... so that sysv4* matches it. echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION} exit 0 ;; i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*) UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'` if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then echo ${UNAME_MACHINE}-univel-sysv${UNAME_REL} else echo ${UNAME_MACHINE}-pc-sysv${UNAME_REL} fi exit 0 ;; i*86:*:5:[78]*) case `/bin/uname -X | grep "^Machine"` in *486*) UNAME_MACHINE=i486 ;; *Pentium) UNAME_MACHINE=i586 ;; *Pent*|*Celeron) UNAME_MACHINE=i686 ;; esac echo ${UNAME_MACHINE}-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION} exit 0 ;; i*86:*:3.2:*) if test -f /usr/options/cb.name; then UNAME_REL=`sed -n 's/.*Version //p' /dev/null >/dev/null ; then UNAME_REL=`(/bin/uname -X|egrep Release|sed -e 's/.*= //')` (/bin/uname -X|egrep i80486 >/dev/null) && UNAME_MACHINE=i486 (/bin/uname -X|egrep '^Machine.*Pentium' >/dev/null) \ && UNAME_MACHINE=i586 (/bin/uname -X|egrep '^Machine.*Pent ?II' >/dev/null) \ && UNAME_MACHINE=i686 (/bin/uname -X|egrep '^Machine.*Pentium Pro' >/dev/null) \ && UNAME_MACHINE=i686 echo ${UNAME_MACHINE}-pc-sco$UNAME_REL else echo ${UNAME_MACHINE}-pc-sysv32 fi exit 0 ;; i*86:*DOS:*:*) echo ${UNAME_MACHINE}-pc-msdosdjgpp exit 0 ;; pc:*:*:*) # Left here for compatibility: # uname -m prints for DJGPP always 'pc', but it prints nothing about # the processor, so we play safe by assuming i386. echo i386-pc-msdosdjgpp exit 0 ;; Intel:Mach:3*:*) echo i386-pc-mach3 exit 0 ;; paragon:*:*:*) echo i860-intel-osf1 exit 0 ;; i860:*:4.*:*) # i860-SVR4 if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then echo i860-stardent-sysv${UNAME_RELEASE} # Stardent Vistra i860-SVR4 else # Add other i860-SVR4 vendors below as they are discovered. echo i860-unknown-sysv${UNAME_RELEASE} # Unknown i860-SVR4 fi exit 0 ;; mini*:CTIX:SYS*5:*) # "miniframe" echo m68010-convergent-sysv exit 0 ;; M68*:*:R3V[567]*:*) test -r /sysV68 && echo 'm68k-motorola-sysv' && exit 0 ;; 3[34]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 4850:*:4.0:3.0) OS_REL='' test -r /etc/.relid \ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid` /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ && echo i486-ncr-sysv4.3${OS_REL} && exit 0 /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ && echo i586-ncr-sysv4.3${OS_REL} && exit 0 ;; 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*) /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ && echo i486-ncr-sysv4 && exit 0 ;; m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*) echo m68k-unknown-lynxos${UNAME_RELEASE} exit 0 ;; mc68030:UNIX_System_V:4.*:*) echo m68k-atari-sysv4 exit 0 ;; i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.0*:*) echo i386-unknown-lynxos${UNAME_RELEASE} exit 0 ;; TSUNAMI:LynxOS:2.*:*) echo sparc-unknown-lynxos${UNAME_RELEASE} exit 0 ;; rs6000:LynxOS:2.*:*) echo rs6000-unknown-lynxos${UNAME_RELEASE} exit 0 ;; PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.0*:*) echo powerpc-unknown-lynxos${UNAME_RELEASE} exit 0 ;; SM[BE]S:UNIX_SV:*:*) echo mips-dde-sysv${UNAME_RELEASE} exit 0 ;; RM*:ReliantUNIX-*:*:*) echo mips-sni-sysv4 exit 0 ;; RM*:SINIX-*:*:*) echo mips-sni-sysv4 exit 0 ;; *:SINIX-*:*:*) if uname -p 2>/dev/null >/dev/null ; then UNAME_MACHINE=`(uname -p) 2>/dev/null` echo ${UNAME_MACHINE}-sni-sysv4 else echo ns32k-sni-sysv fi exit 0 ;; PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort # says echo i586-unisys-sysv4 exit 0 ;; *:UNIX_System_V:4*:FTX*) # From Gerald Hewes . # How about differentiating between stratus architectures? -djm echo hppa1.1-stratus-sysv4 exit 0 ;; *:*:*:FTX*) # From seanf@swdc.stratus.com. echo i860-stratus-sysv4 exit 0 ;; *:VOS:*:*) # From Paul.Green@stratus.com. echo hppa1.1-stratus-vos exit 0 ;; mc68*:A/UX:*:*) echo m68k-apple-aux${UNAME_RELEASE} exit 0 ;; news*:NEWS-OS:6*:*) echo mips-sony-newsos6 exit 0 ;; R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*) if [ -d /usr/nec ]; then echo mips-nec-sysv${UNAME_RELEASE} else echo mips-unknown-sysv${UNAME_RELEASE} fi exit 0 ;; BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only. echo powerpc-be-beos exit 0 ;; BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only. echo powerpc-apple-beos exit 0 ;; BePC:BeOS:*:*) # BeOS running on Intel PC compatible. echo i586-pc-beos exit 0 ;; SX-4:SUPER-UX:*:*) echo sx4-nec-superux${UNAME_RELEASE} exit 0 ;; SX-5:SUPER-UX:*:*) echo sx5-nec-superux${UNAME_RELEASE} exit 0 ;; Power*:Rhapsody:*:*) echo powerpc-apple-rhapsody${UNAME_RELEASE} exit 0 ;; *:Rhapsody:*:*) echo ${UNAME_MACHINE}-apple-rhapsody${UNAME_RELEASE} exit 0 ;; *:Darwin:*:*) echo `uname -p`-apple-darwin${UNAME_RELEASE} exit 0 ;; *:procnto*:*:* | *:QNX:[0123456789]*:*) if test "${UNAME_MACHINE}" = "x86pc"; then UNAME_MACHINE=pc fi echo `uname -p`-${UNAME_MACHINE}-nto-qnx exit 0 ;; *:QNX:*:4*) echo i386-pc-qnx exit 0 ;; NSR-[KW]:NONSTOP_KERNEL:*:*) echo nsr-tandem-nsk${UNAME_RELEASE} exit 0 ;; *:NonStop-UX:*:*) echo mips-compaq-nonstopux exit 0 ;; BS2000:POSIX*:*:*) echo bs2000-siemens-sysv exit 0 ;; DS/*:UNIX_System_V:*:*) echo ${UNAME_MACHINE}-${UNAME_SYSTEM}-${UNAME_RELEASE} exit 0 ;; *:Plan9:*:*) # "uname -m" is not consistent, so use $cputype instead. 386 # is converted to i386 for consistency with other x86 # operating systems. if test "$cputype" = "386"; then UNAME_MACHINE=i386 else UNAME_MACHINE="$cputype" fi echo ${UNAME_MACHINE}-unknown-plan9 exit 0 ;; i*86:OS/2:*:*) # If we were able to find `uname', then EMX Unix compatibility # is probably installed. echo ${UNAME_MACHINE}-pc-os2-emx exit 0 ;; *:TOPS-10:*:*) echo pdp10-unknown-tops10 exit 0 ;; *:TENEX:*:*) echo pdp10-unknown-tenex exit 0 ;; KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*) echo pdp10-dec-tops20 exit 0 ;; XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*) echo pdp10-xkl-tops20 exit 0 ;; *:TOPS-20:*:*) echo pdp10-unknown-tops20 exit 0 ;; *:ITS:*:*) echo pdp10-unknown-its exit 0 ;; i*86:XTS-300:*:STOP) echo ${UNAME_MACHINE}-unknown-stop exit 0 ;; esac #echo '(No uname command or uname output not recognized.)' 1>&2 #echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" 1>&2 cat >$dummy.c < # include #endif main () { #if defined (sony) #if defined (MIPSEB) /* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed, I don't know.... */ printf ("mips-sony-bsd\n"); exit (0); #else #include printf ("m68k-sony-newsos%s\n", #ifdef NEWSOS4 "4" #else "" #endif ); exit (0); #endif #endif #if defined (__arm) && defined (__acorn) && defined (__unix) printf ("arm-acorn-riscix"); exit (0); #endif #if defined (hp300) && !defined (hpux) printf ("m68k-hp-bsd\n"); exit (0); #endif #if defined (NeXT) #if !defined (__ARCHITECTURE__) #define __ARCHITECTURE__ "m68k" #endif int version; version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`; if (version < 4) printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version); else printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version); exit (0); #endif #if defined (MULTIMAX) || defined (n16) #if defined (UMAXV) printf ("ns32k-encore-sysv\n"); exit (0); #else #if defined (CMU) printf ("ns32k-encore-mach\n"); exit (0); #else printf ("ns32k-encore-bsd\n"); exit (0); #endif #endif #endif #if defined (__386BSD__) printf ("i386-pc-bsd\n"); exit (0); #endif #if defined (sequent) #if defined (i386) printf ("i386-sequent-dynix\n"); exit (0); #endif #if defined (ns32000) printf ("ns32k-sequent-dynix\n"); exit (0); #endif #endif #if defined (_SEQUENT_) struct utsname un; uname(&un); if (strncmp(un.version, "V2", 2) == 0) { printf ("i386-sequent-ptx2\n"); exit (0); } if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */ printf ("i386-sequent-ptx1\n"); exit (0); } printf ("i386-sequent-ptx\n"); exit (0); #endif #if defined (vax) # if !defined (ultrix) # include # if defined (BSD) # if BSD == 43 printf ("vax-dec-bsd4.3\n"); exit (0); # else # if BSD == 199006 printf ("vax-dec-bsd4.3reno\n"); exit (0); # else printf ("vax-dec-bsd\n"); exit (0); # endif # endif # else printf ("vax-dec-bsd\n"); exit (0); # endif # else printf ("vax-dec-ultrix\n"); exit (0); # endif #endif #if defined (alliant) && defined (i860) printf ("i860-alliant-bsd\n"); exit (0); #endif exit (1); } EOF eval $set_cc_for_build $CC_FOR_BUILD $dummy.c -o $dummy 2>/dev/null && ./$dummy && rm -f $dummy.c $dummy && exit 0 rm -f $dummy.c $dummy # Apollos put the system type in the environment. test -d /usr/apollo && { echo ${ISP}-apollo-${SYSTYPE}; exit 0; } # Convex versions that predate uname can use getsysinfo(1) if [ -x /usr/convex/getsysinfo ] then case `getsysinfo -f cpu_type` in c1*) echo c1-convex-bsd exit 0 ;; c2*) if getsysinfo -f scalar_acc then echo c32-convex-bsd else echo c2-convex-bsd fi exit 0 ;; c34*) echo c34-convex-bsd exit 0 ;; c38*) echo c38-convex-bsd exit 0 ;; c4*) echo c4-convex-bsd exit 0 ;; esac fi cat >&2 < in order to provide the needed information to handle your system. config.guess timestamp = $timestamp uname -m = `(uname -m) 2>/dev/null || echo unknown` uname -r = `(uname -r) 2>/dev/null || echo unknown` uname -s = `(uname -s) 2>/dev/null || echo unknown` uname -v = `(uname -v) 2>/dev/null || echo unknown` /usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null` /bin/uname -X = `(/bin/uname -X) 2>/dev/null` hostinfo = `(hostinfo) 2>/dev/null` /bin/universe = `(/bin/universe) 2>/dev/null` /usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null` /bin/arch = `(/bin/arch) 2>/dev/null` /usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null` /usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null` UNAME_MACHINE = ${UNAME_MACHINE} UNAME_RELEASE = ${UNAME_RELEASE} UNAME_SYSTEM = ${UNAME_SYSTEM} UNAME_VERSION = ${UNAME_VERSION} EOF exit 1 # Local variables: # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "timestamp='" # time-stamp-format: "%:y-%02m-%02d" # time-stamp-end: "'" # End: tree-puzzle-5.2/install-sh0000755000076400001440000001267107470534437011357 #!/bin/sh # # install - install a program, script, or datafile # This comes from X11R5 (mit/util/scripts/install.sh). # # Copyright 1991 by the Massachusetts Institute of Technology # # Permission to use, copy, modify, distribute, and sell this software and its # documentation for any purpose is hereby granted without fee, provided that # the above copyright notice appear in all copies and that both that # copyright notice and this permission notice appear in supporting # documentation, and that the name of M.I.T. not be used in advertising or # publicity pertaining to distribution of the software without specific, # written prior permission. M.I.T. makes no representations about the # suitability of this software for any purpose. It is provided "as is" # without express or implied warranty. # # Calling this script install-sh is preferred over install.sh, to prevent # `make' implicit rules from creating a file called install from it # when there is no Makefile. # # This script is compatible with the BSD install script, but was written # from scratch. It can only install one file at a time, a restriction # shared with many OS's install programs. # set DOITPROG to echo to test this script # Don't use :- since 4.3BSD and earlier shells don't like it. doit="${DOITPROG-}" # put in absolute paths if you don't have them in your path; or use env. vars. mvprog="${MVPROG-mv}" cpprog="${CPPROG-cp}" chmodprog="${CHMODPROG-chmod}" chownprog="${CHOWNPROG-chown}" chgrpprog="${CHGRPPROG-chgrp}" stripprog="${STRIPPROG-strip}" rmprog="${RMPROG-rm}" mkdirprog="${MKDIRPROG-mkdir}" transformbasename="" transform_arg="" instcmd="$mvprog" chmodcmd="$chmodprog 0755" chowncmd="" chgrpcmd="" stripcmd="" rmcmd="$rmprog -f" mvcmd="$mvprog" src="" dst="" dir_arg="" while [ x"$1" != x ]; do case $1 in -c) instcmd="$cpprog" shift continue;; -d) dir_arg=true shift continue;; -m) chmodcmd="$chmodprog $2" shift shift continue;; -o) chowncmd="$chownprog $2" shift shift continue;; -g) chgrpcmd="$chgrpprog $2" shift shift continue;; -s) stripcmd="$stripprog" shift continue;; -t=*) transformarg=`echo $1 | sed 's/-t=//'` shift continue;; -b=*) transformbasename=`echo $1 | sed 's/-b=//'` shift continue;; *) if [ x"$src" = x ] then src=$1 else # this colon is to work around a 386BSD /bin/sh bug : dst=$1 fi shift continue;; esac done if [ x"$src" = x ] then echo "install: no input file specified" exit 1 else : fi if [ x"$dir_arg" != x ]; then dst=$src src="" if [ -d $dst ]; then instcmd=: chmodcmd="" else instcmd=$mkdirprog fi else # Waiting for this to be detected by the "$instcmd $src $dsttmp" command # might cause directories to be created, which would be especially bad # if $src (and thus $dsttmp) contains '*'. if [ -f $src -o -d $src ] then : else echo "install: $src does not exist" exit 1 fi if [ x"$dst" = x ] then echo "install: no destination specified" exit 1 else : fi # If destination is a directory, append the input filename; if your system # does not like double slashes in filenames, you may need to add some logic if [ -d $dst ] then dst="$dst"/`basename $src` else : fi fi ## this sed command emulates the dirname command dstdir=`echo $dst | sed -e 's,[^/]*$,,;s,/$,,;s,^$,.,'` # Make sure that the destination directory exists. # this part is taken from Noah Friedman's mkinstalldirs script # Skip lots of stat calls in the usual case. if [ ! -d "$dstdir" ]; then defaultIFS=' ' IFS="${IFS-${defaultIFS}}" oIFS="${IFS}" # Some sh's can't handle IFS=/ for some reason. IFS='%' set - `echo ${dstdir} | sed -e 's@/@%@g' -e 's@^%@/@'` IFS="${oIFS}" pathcomp='' while [ $# -ne 0 ] ; do pathcomp="${pathcomp}${1}" shift if [ ! -d "${pathcomp}" ] ; then $mkdirprog "${pathcomp}" else : fi pathcomp="${pathcomp}/" done fi if [ x"$dir_arg" != x ] then $doit $instcmd $dst && if [ x"$chowncmd" != x ]; then $doit $chowncmd $dst; else : ; fi && if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd $dst; else : ; fi && if [ x"$stripcmd" != x ]; then $doit $stripcmd $dst; else : ; fi && if [ x"$chmodcmd" != x ]; then $doit $chmodcmd $dst; else : ; fi else # If we're going to rename the final executable, determine the name now. if [ x"$transformarg" = x ] then dstfile=`basename $dst` else dstfile=`basename $dst $transformbasename | sed $transformarg`$transformbasename fi # don't allow the sed command to completely eliminate the filename if [ x"$dstfile" = x ] then dstfile=`basename $dst` else : fi # Make a temp file name in the proper directory. dsttmp=$dstdir/#inst.$$# # Move or copy the file name to the temp name $doit $instcmd $src $dsttmp && trap "rm -f ${dsttmp}" 0 && # and set any options; do chmod last to preserve setuid bits # If any of these fail, we abort the whole thing. If we want to # ignore errors from any of these, just make sure not to ignore # errors from the above "$doit $instcmd $src $dsttmp" command. if [ x"$chowncmd" != x ]; then $doit $chowncmd $dsttmp; else :;fi && if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd $dsttmp; else :;fi && if [ x"$stripcmd" != x ]; then $doit $stripcmd $dsttmp; else :;fi && if [ x"$chmodcmd" != x ]; then $doit $chmodcmd $dsttmp; else :;fi && # Now rename the file to the real destination. $doit $rmcmd -f $dstdir/$dstfile && $doit $mvcmd $dsttmp $dstdir/$dstfile fi && exit 0 tree-puzzle-5.2/config.sub0000755000076400001440000006700507410242741011323 #! /bin/sh # Configuration validation subroutine script. # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001 # Free Software Foundation, Inc. timestamp='2001-08-13' # This file is (in principle) common to ALL GNU software. # The presence of a machine in this file suggests that SOME GNU software # can handle that machine. It does not imply ALL GNU software can. # # This file is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place - Suite 330, # Boston, MA 02111-1307, USA. # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that program. # Please send patches to . # # Configuration subroutine to validate and canonicalize a configuration type. # Supply the specified configuration type as an argument. # If it is invalid, we print an error message on stderr and exit with code 1. # Otherwise, we print the canonical config type on stdout and succeed. # This file is supposed to be the same for all GNU packages # and recognize all the CPU types, system types and aliases # that are meaningful with *any* GNU software. # Each package is responsible for reporting which valid configurations # it does not support. The user should be able to distinguish # a failure to support a valid configuration from a meaningless # configuration. # The goal of this file is to map all the various variations of a given # machine specification into a single specification in the form: # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM # or in some cases, the newer four-part form: # CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM # It is wrong to echo any other type of specification. me=`echo "$0" | sed -e 's,.*/,,'` usage="\ Usage: $0 [OPTION] CPU-MFR-OPSYS $0 [OPTION] ALIAS Canonicalize a configuration name. Operation modes: -h, --help print this help, then exit -t, --time-stamp print date of last modification, then exit -v, --version print version number, then exit Report bugs and patches to ." version="\ GNU config.sub ($timestamp) Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." help=" Try \`$me --help' for more information." # Parse command line while test $# -gt 0 ; do case $1 in --time-stamp | --time* | -t ) echo "$timestamp" ; exit 0 ;; --version | -v ) echo "$version" ; exit 0 ;; --help | --h* | -h ) echo "$usage"; exit 0 ;; -- ) # Stop option processing shift; break ;; - ) # Use stdin as input. break ;; -* ) echo "$me: invalid option $1$help" exit 1 ;; *local*) # First pass through any local machine types. echo $1 exit 0;; * ) break ;; esac done case $# in 0) echo "$me: missing argument$help" >&2 exit 1;; 1) ;; *) echo "$me: too many arguments$help" >&2 exit 1;; esac # Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any). # Here we must recognize all the valid KERNEL-OS combinations. maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'` case $maybe_os in nto-qnx* | linux-gnu* | storm-chaos* | os2-emx* | windows32-*) os=-$maybe_os basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'` ;; *) basic_machine=`echo $1 | sed 's/-[^-]*$//'` if [ $basic_machine != $1 ] then os=`echo $1 | sed 's/.*-/-/'` else os=; fi ;; esac ### Let's recognize common machines as not being operating systems so ### that things like config.sub decstation-3100 work. We also ### recognize some manufacturers as not being operating systems, so we ### can provide default operating systems below. case $os in -sun*os*) # Prevent following clause from handling this invalid input. ;; -dec* | -mips* | -sequent* | -encore* | -pc532* | -sgi* | -sony* | \ -att* | -7300* | -3300* | -delta* | -motorola* | -sun[234]* | \ -unicom* | -ibm* | -next | -hp | -isi* | -apollo | -altos* | \ -convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\ -c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \ -harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \ -apple | -axis) os= basic_machine=$1 ;; -sim | -cisco | -oki | -wec | -winbond) os= basic_machine=$1 ;; -scout) ;; -wrs) os=-vxworks basic_machine=$1 ;; -chorusos*) os=-chorusos basic_machine=$1 ;; -chorusrdb) os=-chorusrdb basic_machine=$1 ;; -hiux*) os=-hiuxwe2 ;; -sco5) os=-sco3.2v5 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco4) os=-sco3.2v4 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco3.2.[4-9]*) os=`echo $os | sed -e 's/sco3.2./sco3.2v/'` basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco3.2v[4-9]*) # Don't forget version if it is 3.2v4 or newer. basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco*) os=-sco3.2v2 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -udk*) basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -isc) os=-isc2.2 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -clix*) basic_machine=clipper-intergraph ;; -isc*) basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -lynx*) os=-lynxos ;; -ptx*) basic_machine=`echo $1 | sed -e 's/86-.*/86-sequent/'` ;; -windowsnt*) os=`echo $os | sed -e 's/windowsnt/winnt/'` ;; -psos*) os=-psos ;; -mint | -mint[0-9]*) basic_machine=m68k-atari os=-mint ;; esac # Decode aliases for certain CPU-COMPANY combinations. case $basic_machine in # Recognize the basic CPU types without company name. # Some are omitted here because they have special meanings below. 1750a | 580 \ | a29k \ | alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \ | arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr \ | c4x | clipper \ | d10v | d30v | dsp16xx \ | fr30 \ | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \ | i370 | i860 | i960 | ia64 \ | m32r | m68000 | m68k | m88k | mcore \ | mips16 | mips64 | mips64el | mips64orion | mips64orionel \ | mips64vr4100 | mips64vr4100el | mips64vr4300 \ | mips64vr4300el | mips64vr5000 | mips64vr5000el \ | mipsbe | mipsel | mipsle | mipstx39 | mipstx39el \ | mn10200 | mn10300 \ | ns16k | ns32k \ | openrisc \ | pdp10 | pdp11 | pj | pjl \ | powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \ | pyramid \ | s390 | s390x \ | sh | sh[34] | sh[34]eb | shbe | shle \ | sparc | sparc64 | sparclet | sparclite | sparcv9 | sparcv9b \ | strongarm \ | tahoe | thumb | tic80 | tron \ | v850 \ | we32k \ | x86 | xscale \ | z8k) basic_machine=$basic_machine-unknown ;; m6811 | m68hc11 | m6812 | m68hc12) # Motorola 68HC11/12. basic_machine=$basic_machine-unknown os=-none ;; m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65 | z8k) ;; # We use `pc' rather than `unknown' # because (1) that's what they normally are, and # (2) the word "unknown" tends to confuse beginning users. i*86 | x86_64) basic_machine=$basic_machine-pc ;; # Object if more than one company name word. *-*-*) echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2 exit 1 ;; # Recognize the basic CPU types with company name. 580-* \ | a29k-* \ | alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \ | alphapca5[67]-* | arc-* \ | arm-* | armbe-* | armle-* | armv*-* \ | bs2000-* \ | c[123]* | c30-* | [cjt]90-* | c54x-* \ | clipper-* | cray2-* | cydra-* \ | d10v-* | d30v-* \ | elxsi-* \ | f30[01]-* | f700-* | fr30-* | fx80-* \ | h8300-* | h8500-* \ | hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \ | i*86-* | i860-* | i960-* | ia64-* \ | m32r-* \ | m68000-* | m680[01234]0-* | m68360-* | m683?2-* | m68k-* \ | m88110-* | m88k-* | mcore-* \ | mips-* | mips16-* | mips64-* | mips64el-* | mips64orion-* \ | mips64orionel-* | mips64vr4100-* | mips64vr4100el-* \ | mips64vr4300-* | mips64vr4300el-* | mipsbe-* | mipsel-* \ | mipsle-* | mipstx39-* | mipstx39el-* \ | none-* | np1-* | ns16k-* | ns32k-* \ | orion-* \ | pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \ | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \ | pyramid-* \ | romp-* | rs6000-* \ | s390-* | s390x-* \ | sh-* | sh[34]-* | sh[34]eb-* | shbe-* | shle-* \ | sparc-* | sparc64-* | sparc86x-* | sparclite-* \ | sparcv9-* | sparcv9b-* | strongarm-* | sv1-* \ | t3e-* | tahoe-* | thumb-* | tic30-* | tic54x-* | tic80-* | tron-* \ | v850-* | vax-* \ | we32k-* \ | x86-* | x86_64-* | xmp-* | xps100-* | xscale-* \ | ymp-* \ | z8k-*) ;; # Recognize the various machine names and aliases which stand # for a CPU type and a company and sometimes even an OS. 386bsd) basic_machine=i386-unknown os=-bsd ;; 3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc) basic_machine=m68000-att ;; 3b*) basic_machine=we32k-att ;; a29khif) basic_machine=a29k-amd os=-udi ;; adobe68k) basic_machine=m68010-adobe os=-scout ;; alliant | fx80) basic_machine=fx80-alliant ;; altos | altos3068) basic_machine=m68k-altos ;; am29k) basic_machine=a29k-none os=-bsd ;; amdahl) basic_machine=580-amdahl os=-sysv ;; amiga | amiga-*) basic_machine=m68k-unknown ;; amigaos | amigados) basic_machine=m68k-unknown os=-amigaos ;; amigaunix | amix) basic_machine=m68k-unknown os=-sysv4 ;; apollo68) basic_machine=m68k-apollo os=-sysv ;; apollo68bsd) basic_machine=m68k-apollo os=-bsd ;; aux) basic_machine=m68k-apple os=-aux ;; balance) basic_machine=ns32k-sequent os=-dynix ;; convex-c1) basic_machine=c1-convex os=-bsd ;; convex-c2) basic_machine=c2-convex os=-bsd ;; convex-c32) basic_machine=c32-convex os=-bsd ;; convex-c34) basic_machine=c34-convex os=-bsd ;; convex-c38) basic_machine=c38-convex os=-bsd ;; cray | ymp) basic_machine=ymp-cray os=-unicos ;; cray2) basic_machine=cray2-cray os=-unicos ;; [cjt]90) basic_machine=${basic_machine}-cray os=-unicos ;; crds | unos) basic_machine=m68k-crds ;; cris | cris-* | etrax*) basic_machine=cris-axis ;; da30 | da30-*) basic_machine=m68k-da30 ;; decstation | decstation-3100 | pmax | pmax-* | pmin | dec3100 | decstatn) basic_machine=mips-dec ;; delta | 3300 | motorola-3300 | motorola-delta \ | 3300-motorola | delta-motorola) basic_machine=m68k-motorola ;; delta88) basic_machine=m88k-motorola os=-sysv3 ;; dpx20 | dpx20-*) basic_machine=rs6000-bull os=-bosx ;; dpx2* | dpx2*-bull) basic_machine=m68k-bull os=-sysv3 ;; ebmon29k) basic_machine=a29k-amd os=-ebmon ;; elxsi) basic_machine=elxsi-elxsi os=-bsd ;; encore | umax | mmax) basic_machine=ns32k-encore ;; es1800 | OSE68k | ose68k | ose | OSE) basic_machine=m68k-ericsson os=-ose ;; fx2800) basic_machine=i860-alliant ;; genix) basic_machine=ns32k-ns ;; gmicro) basic_machine=tron-gmicro os=-sysv ;; go32) basic_machine=i386-pc os=-go32 ;; h3050r* | hiux*) basic_machine=hppa1.1-hitachi os=-hiuxwe2 ;; h8300hms) basic_machine=h8300-hitachi os=-hms ;; h8300xray) basic_machine=h8300-hitachi os=-xray ;; h8500hms) basic_machine=h8500-hitachi os=-hms ;; harris) basic_machine=m88k-harris os=-sysv3 ;; hp300-*) basic_machine=m68k-hp ;; hp300bsd) basic_machine=m68k-hp os=-bsd ;; hp300hpux) basic_machine=m68k-hp os=-hpux ;; hp3k9[0-9][0-9] | hp9[0-9][0-9]) basic_machine=hppa1.0-hp ;; hp9k2[0-9][0-9] | hp9k31[0-9]) basic_machine=m68000-hp ;; hp9k3[2-9][0-9]) basic_machine=m68k-hp ;; hp9k6[0-9][0-9] | hp6[0-9][0-9]) basic_machine=hppa1.0-hp ;; hp9k7[0-79][0-9] | hp7[0-79][0-9]) basic_machine=hppa1.1-hp ;; hp9k78[0-9] | hp78[0-9]) # FIXME: really hppa2.0-hp basic_machine=hppa1.1-hp ;; hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893) # FIXME: really hppa2.0-hp basic_machine=hppa1.1-hp ;; hp9k8[0-9][13679] | hp8[0-9][13679]) basic_machine=hppa1.1-hp ;; hp9k8[0-9][0-9] | hp8[0-9][0-9]) basic_machine=hppa1.0-hp ;; hppa-next) os=-nextstep3 ;; hppaosf) basic_machine=hppa1.1-hp os=-osf ;; hppro) basic_machine=hppa1.1-hp os=-proelf ;; i370-ibm* | ibm*) basic_machine=i370-ibm ;; # I'm not sure what "Sysv32" means. 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mips3*) basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`-unknown ;; mmix*) basic_machine=mmix-knuth os=-mmixware ;; monitor) basic_machine=m68k-rom68k os=-coff ;; msdos) basic_machine=i386-pc os=-msdos ;; mvs) basic_machine=i370-ibm os=-mvs ;; ncr3000) basic_machine=i486-ncr os=-sysv4 ;; netbsd386) basic_machine=i386-unknown os=-netbsd ;; netwinder) basic_machine=armv4l-rebel os=-linux ;; news | news700 | news800 | news900) basic_machine=m68k-sony os=-newsos ;; news1000) basic_machine=m68030-sony os=-newsos ;; news-3600 | risc-news) basic_machine=mips-sony os=-newsos ;; necv70) basic_machine=v70-nec os=-sysv ;; next | m*-next ) basic_machine=m68k-next case $os in -nextstep* ) ;; -ns2*) os=-nextstep2 ;; *) os=-nextstep3 ;; esac ;; nh3000) basic_machine=m68k-harris os=-cxux ;; nh[45]000) basic_machine=m88k-harris os=-cxux ;; nindy960) basic_machine=i960-intel os=-nindy ;; mon960) basic_machine=i960-intel os=-mon960 ;; nonstopux) basic_machine=mips-compaq os=-nonstopux ;; np1) basic_machine=np1-gould ;; nsr-tandem) basic_machine=nsr-tandem ;; op50n-* | op60c-*) basic_machine=hppa1.1-oki os=-proelf ;; OSE68000 | ose68000) basic_machine=m68000-ericsson os=-ose ;; os68k) basic_machine=m68k-none os=-os68k ;; pa-hitachi) basic_machine=hppa1.1-hitachi os=-hiuxwe2 ;; paragon) basic_machine=i860-intel os=-osf ;; pbd) basic_machine=sparc-tti ;; pbb) basic_machine=m68k-tti ;; pc532 | pc532-*) basic_machine=ns32k-pc532 ;; pentium | p5 | k5 | k6 | nexgen) basic_machine=i586-pc ;; pentiumpro | p6 | 6x86 | athlon) basic_machine=i686-pc ;; pentiumii | pentium2) basic_machine=i686-pc ;; pentium-* | p5-* | k5-* | k6-* | nexgen-*) basic_machine=i586-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pentiumpro-* | p6-* | 6x86-* | athlon-*) basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pentiumii-* | pentium2-*) basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pn) basic_machine=pn-gould ;; power) basic_machine=power-ibm ;; ppc) basic_machine=powerpc-unknown ;; ppc-*) basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'` ;; ppcle | powerpclittle | ppc-le | powerpc-little) basic_machine=powerpcle-unknown ;; ppcle-* | powerpclittle-*) basic_machine=powerpcle-`echo $basic_machine | sed 's/^[^-]*-//'` ;; ppc64) basic_machine=powerpc64-unknown ;; ppc64-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'` ;; ppc64le | powerpc64little | ppc64-le | powerpc64-little) basic_machine=powerpc64le-unknown ;; ppc64le-* | powerpc64little-*) basic_machine=powerpc64le-`echo $basic_machine | sed 's/^[^-]*-//'` ;; ps2) basic_machine=i386-ibm ;; pw32) basic_machine=i586-unknown os=-pw32 ;; rom68k) basic_machine=m68k-rom68k os=-coff ;; rm[46]00) basic_machine=mips-siemens ;; rtpc | rtpc-*) basic_machine=romp-ibm ;; sa29200) basic_machine=a29k-amd os=-udi ;; sequent) basic_machine=i386-sequent ;; sh) basic_machine=sh-hitachi os=-hms ;; sparclite-wrs) basic_machine=sparclite-wrs os=-vxworks ;; sps7) basic_machine=m68k-bull os=-sysv2 ;; spur) basic_machine=spur-unknown ;; st2000) basic_machine=m68k-tandem ;; stratus) basic_machine=i860-stratus os=-sysv4 ;; sun2) basic_machine=m68000-sun ;; sun2os3) basic_machine=m68000-sun os=-sunos3 ;; sun2os4) basic_machine=m68000-sun os=-sunos4 ;; sun3os3) basic_machine=m68k-sun os=-sunos3 ;; sun3os4) basic_machine=m68k-sun os=-sunos4 ;; sun4os3) basic_machine=sparc-sun os=-sunos3 ;; sun4os4) basic_machine=sparc-sun os=-sunos4 ;; sun4sol2) basic_machine=sparc-sun os=-solaris2 ;; sun3 | sun3-*) basic_machine=m68k-sun ;; sun4) basic_machine=sparc-sun ;; sun386 | sun386i | roadrunner) basic_machine=i386-sun ;; sv1) basic_machine=sv1-cray os=-unicos ;; symmetry) basic_machine=i386-sequent os=-dynix ;; t3e) basic_machine=t3e-cray os=-unicos ;; tic54x | c54x*) basic_machine=tic54x-unknown os=-coff ;; tx39) basic_machine=mipstx39-unknown ;; tx39el) basic_machine=mipstx39el-unknown ;; tower | tower-32) basic_machine=m68k-ncr ;; udi29k) basic_machine=a29k-amd os=-udi ;; ultra3) basic_machine=a29k-nyu os=-sym1 ;; v810 | necv810) basic_machine=v810-nec os=-none ;; vaxv) basic_machine=vax-dec os=-sysv ;; vms) basic_machine=vax-dec os=-vms ;; vpp*|vx|vx-*) basic_machine=f301-fujitsu ;; vxworks960) basic_machine=i960-wrs os=-vxworks ;; vxworks68) basic_machine=m68k-wrs os=-vxworks ;; vxworks29k) basic_machine=a29k-wrs os=-vxworks ;; w65*) basic_machine=w65-wdc os=-none ;; w89k-*) basic_machine=hppa1.1-winbond os=-proelf ;; windows32) basic_machine=i386-pc os=-windows32-msvcrt ;; xmp) basic_machine=xmp-cray os=-unicos ;; xps | xps100) basic_machine=xps100-honeywell ;; z8k-*-coff) basic_machine=z8k-unknown os=-sim ;; none) basic_machine=none-none os=-none ;; # Here we handle the default manufacturer of certain CPU types. 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Schmidt, Korbinian Strimmer, Martin Vingron, Arndt von Haeseler 1995-1999 by Korbinian Strimmer and Arndt von Haeseler ($Id$) Heiko A. Schmidt MPI for Molecular Genetics Computational Molecular Biology Ihnestrasse 73 D-14195 Berlin Germany email: hschmidt@molgen.mpg.de, http://cmb.molgen.mpg.de Korbinian Strimmer Department of Statistics University of Munich Ludwigstrasse 33 D-80539 Munich Germany email: strimmer@stat.uni-muenchen.de http://www.stat.uni-muenchen.de/~strimmer/ Martin Vingron MPI for Molecular Genetics Computational Molecular Biology Ihnestrasse 73 D-14195 Berlin Germany email: vingron@molgen.mpg.de, http://cmb.molgen.mpg.de Arndt von Haeseler HHU Duesseldorf Mathematisches Institut Abteilung fuer Informatik Universitaetsstr. 1 D-40225 Duesseldorf Germany email: haeseler@cs.uni-duesseldorf.de http://www.cs.uni-duesseldorf.de/~haeseler/ and John-von-Neumann Institut fuer Computing Forschungsgruppe Bioinformatik FZ-Juelich D-52425 Juelich Germany tree-puzzle-5.2/INSTALL0000644000076400001440000002230607470534437010400 Copyright 1994, 1995, 1996, 1999, 2000, 2001 Free Software Foundation, Inc. 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Usually `configure' can determine that directory automatically. `configure' also accepts some other, not widely useful, options. Run `configure --help' for more details. tree-puzzle-5.2/ChangeLog0000644000076400001440000007332010075305236011107 ChangeLog ($Id$) Version date what has been changed TODO: missing quartet handling missing quartet counting in parallel case DONE: 5.2 14.07.2004 - Version 5.2 !!! NEW RELEASE =========== 5.2.rc17 14.07.2004 - Manual sources moved out of the package - numerous changes in the manual 5.2.rc16 12.07.2004 - Makefile.am: double distclean rule removed - fflush added before mygets() - because of Windows - manual spell-checked - '-consmrel' fixed - usage message extended 5.2.rc15 09.07.2004 - many changes to the manual 5.2.rc14 01.07.2004 - test suite checked, notice about results added 5.2.rc13 01.07.2004 - a number of small fixes (alloc and dealloc in epe) - convergence output for user branches fixed - G-T rate output precision fixed - tests checked and fixed 5.2.rc12 30.06.2004 - branch length convergence output corrected for user set branch lengths (i.e. no estimate) - avergedist updated: output of min/max/var/std.dev. - tstvratio and yrtsratio - no output for GTR - some future cmdline flags added to help - -prefix, -sub50, -randseed moved to usage output - -randseed=# added - release date changed in code 5.2.rc11 18.06.2004 - flags to set epsilon values added for debugging (dependent on USE_ADJUSTABLE_EPS compiler switch) 19.06.2004 - quartet percent computation fixed: quartet sums moved qinfomatr[0] -> qinfomatr[8] qinfomatr[0]=missing qs. (release 5.2.rc9) - character state output added to R/Q matrix output - average computation of dist-matrix changed: mean=average, variance, std deviation TODO: proper output / use Korbis S.E. method 25.06.2004 - GTR model ready, menu order HKY, TN, GTR, (SH), HKY 29.06.2004 - many changes to the manual 5.2.rc10 11.06.2004 - fixed no quartets in parameter estimtion for <4 seqs 15.06.2004 - computation of Bayesian weights moved into subroutine loglkl2weight. - use subroutine loglkl2weight in parallel code -> fixing division by zero bug 5.2.rc9 11.06.2004 - sequence number check for <4 and >257 added <4 - no quartet methods available >257 - no quartet puzzling available - counting for missing quartets added for parallel message checking (TODO: handling and checking) - output of root branch name added for clock analysis (sequence name or "internal branch") 5.2.rc8 04.05.2004 - tree tests move to treetest.c/treetest.h - comments added - typo corrected (suset -> subset) 08.06.2004 - ELW: continue counting p, when significantly worse - 1sKH/2sKH: restrict tests to 3 digits (0.00) (test behaviour: seems not to use some trees (KH), see above - used, but too low variance) 5.2.rc7 12.02.2004 - corrected typos in usage/README 20.02.2004 - cmdline: prefix flag fixed 22.02.2004 - '-wsr/-wsl' flags fixed: output file and file name output 5.2.rc6 25.11.2003 - 'FPRINTF...' changed to 'fprintf(STDOUT,' - strcpy added in openfile-routines 5.2.rc5 25.11.2003 - filename length chack added - typo FILENAMELENTH corrected 5.2.rc4 19.11.2003 - minor corrections: int/uli comparisons - SPRNG added to src/sprng - src/sprng autoconf/automake setup - Parallel Parameter Estimation (JPDC, Ekki 1) 5.2.rc3 07.11.2003 - WAG Matrix code/docu corrected (Goldman) TODO: remove additional output for printrmat TODO: make PEPS* smaller to have better accuracy in parameter estimation. 5.2.rc2 01.09.2003 - bug from 5.1.pl29 found and eliminated alloc size wrong: worked if Maxsubset<=Maxspc TODO: remove out-commented debug messages 5.2.rc1 20.08.2003 - first release candidate for tree-puzzle 5.2 CODE FREEZE =========== 5.1.pl30 20.08.2003 - naming convention changed for manual name input to use FILENAME.puzzle, ... 5.1.pl29 23.07.2003 - new compiler warnings fixed - index error naming fixed - debugging of matrix based permutation (not finished) 5.1.pl28 01.07.2003 - cmdline flags to switch off ml branch lengths (-notreelh), tree tests (-notreetest) 5.1.pl27 24.06.2003 - output quartet support for incorporated split in report file 5.1.pl26 06.06.2003 - menu order of tree reconstruction methods altered to QP, user tree, consensus, dist (no tree) (last two switched) 5.1.pl25 05.06.2003 - small changes to fix compiler warnings 5.1.pl24 04.06.2003 - changes from benchmark-branch merged: debug output removed - checktime fixed: sumtodo <-> done for quartets 5.1.pl23 26.05.2003 - puzzle.c: CONSENSUS -> QUARTPUZ, allocated unnecessary memory - additional malloc-checks added (if buffer == NULL) 01.06.2003 - mlmode conditions with readable constants (ml2.c,ml.h) - garbage collection in tree2bipart/subtree2bipart 5.1.pl22 16.05.2003 - fixing Array Bound Read in fputid (bug had no effect, but was read before check) - garbage collection completed in p-step algorithms and node-label (free_tree/internalnode), trueIDtmp (allpstep), - small fix in test script and rebuild of check-files 5.1.pl21 14.05.2003 - fixing free of all allocations in puzzling step (mrca, recur, split, orig) 5.1.pl20 05.05.2003 - small fix in recursive Alg. (recur.c) - debug output removed - cross check removed from (recur.c,mrca.c) 5.1.pl19 27.04.2003 - recursive Alg. (recur.c) fixed: edge cluster has not to be reconstructed after adding new leaves only updated. - debug output removed from recur.c, split.c - MRCA-based (mrca.c) finished 5.1.pl18 26.04.2003 - recursive (recur.c) finished TODO: remove debug output - MRCA (mrca.c) startet 5.1.pl17 25.04.2003 - split-based (split.c) finished TODO: remove debug output - recursive (recur.c) startet 5.1.pl16 22.04.2003 - orig pstep alg: updating of edgemap outsourced to updateedgemap_orig - writeOTU_orig, writetree_orig, resetedgeinfo_orig, minimumedgeinfo_orig: _orig removed, since independent of algorithm type - onepstep: _orig added (onepstep_orig) - time check/status output moved to checktime routine. added to ml step of parallel version - split.c temporarily added to release 5.1.pl15 18.04.2003 - trueID dependent procedures 'de-trueID-ed' trueID saved in the tips of the tree. 5.1.pl14 10.04.2003 - consensus stuff moved to consensus.h/.c - unique tree sorting moved to treesort.h/.c - changes to pstep-split.h/.c - changed names of procedures using trueID to *_trueID 5.1.pl13 07.04.2003 - subsetmatr.[hc] added to process missing data analyses. (old version, functions in puzzle2) - deglobalized: guessdatatype, readsequencefile, getsizesites, initid, getseqs removed obsolete: getdataset - moved: output of taxa after input - computation of Maxbrnch moved from readsequencefile to inputandinit - readsubsetfile, permutetaxa_ss added, '-rssm' works - empty quartets fixed in checkquartet missing data -> OK, HALT error otherwise 5.1.pl12 04.04.2003 - tests: check-qp-clock regenerated, changes in Makefile.am and template-test - obsolete stuff removed: global trueID_orig + alloc, inittree_orig/freetree_orig from PP_SendDoPermutBlock PP_slave_do_puzzling (ppuzzle), global _orig variables (pstep), makenewsplitentries (old), kh_test (old) - column variable in tree output routines deglobalized - copyright headers added to pstep.[hc] - pstep copied to pstep-{split | mrca | recursive} - implementation of pstep-split.[ch] started (done: structure/init, todo: remove _orig stuff) 5.1.pl11 03.04.2003 - tests/Makefile.am: 'build-puzzle failed' fixed - some changes in test script template - cleanup: removed obsolete routines - puzzle module: makenewsplitentriesnew - ppuzzle module: PP_do_puzzling, PP_SendPermut, PP_RecvPermut, PP_SendSplits, PP_RecvSplits - deglobalized: makenewsplitentries, makepart, computebiparts, copysplit - parallel puzzling step based on allpstep, onepstep - time check/status output added to parallel version (inaccurate since current slave progress not known) - TIMECHECK_INTERVAL for setting time interval of status output in ML/puzzling step - Header when printing 1 PAM rate matrix (-printrmat) - final pstep copied to pstep-{split | mrca | recursive} 5.1.pl10 02.04.2003 - tests/Makefile.am fixed (TODO: build-puzzle.test) - Dates/Version adjusted: April 2003/TREE-PUZZLE 5.2 - Dates/Version fixed in doc/*.html, doc/*.tex - number added to outgroup(menu)/sequence(start) output - Time measurement only done after each completed intermediate tree to reduce the the number from O(Numtrial*n^4) to O(Numtrial) -> less overhead, but 15min met less accurate. - quartet support output for splits added in writeoutputfile for later use (TODO: '#if0'ed) - (sequential) puzzling step moved from puzzle1.c to pstep.c: allpstep, onepstep TODO: parallel puzzling step in ppuzzle.c (works but with old PP_slave_do_puzzling) 5.1.pl9 31.03.2003 - consensus construction added to menu - support value computation fixed for phylip tree, wrong divisor used in consensus - test directory/Makefile.am/tests created (make check) 5.1.pl8 30.03.2003 - puzzling step proc's: most variables 'deglobalized' 5.1.pl7 26.03.2003 - original puzzling step out-sourced to pstep-orig.c and pstep-orig.h pstep.c, pstep.h (and above) added to Makefile.am 5.1.pl6 25.03.2003 - '-usebranch' option added fr later use - 'SONJA' added for external parameter estimation 5.1.pl5 24.03.2003 - ml branch length estimation added to consensus option (todo: plausibility check - is tree file available) - output for reportfile fixed - output of likelihood to clocklike tree in treefile added/fixed 5.1.pl4 21.03.2003 - consensus option added to compute usertree consensus (only consensus is computed and printed to stdin) - usertreefile PREFIX fixed 5.1.pl3 20.03.2003 - TP_MAX_EXP_DIFF=b-a>0 introduced, such that (1.0+exp(a-b) == 1.0) to avoid the computation as well as possible FPE, when a-b gets very small. - flag '-prefix=XXX' added: use 'XXX' as filename prefix instead of 'Infilename' 5.1.pl2 05.12.2002 - PP_Finalized before exit in parallel programs. 5.1.pl1 05.12.2002 - FPE in Brent's algorithm fixed: ()/0, when x=w=v. 5.1 05.11.2002 - Version 5.1 !!! NEW RELEASE =========== 5.1.rc9 02.11.2002 - CPBI datasets (EF.phy, EF.3trees) added to data - manual updates (statistics, Acknowledgments) - latex2html added to Makefile.am - Date changed from September to November 2002 5.1.rc8 24.10.2002 - manual updated: quartet statistics, gap/ambiguous character statistics, 1sKH, 2sKH, SH test, ELW. - fixes in manual (not finished: XXX) 5.1.rc7 24.10.2002 - printversion: ALPHA compiler warning fixed - HHH only for unimplemented stuff 5.1.rc6 15.09.2002 - small fixes: compiler warnings fixed - debug output removed - 2sKH moved to the end of test output (1sKH, SH, ELW, 2sHK) - save site rates ('-wsr') added 5.1.rc5 15.09.2002 - small fixes: printf -> PRINTF 5.1.rc4 10.09.2002 - site likelihoods output to file added (PHYLIP-like) TODO: binary - in preparation:-wslb, -wparam, -usebranch, -rssm, -consensus 5.1.rc3 10.09.2002 - SH test, ELW test added. - one sided KH test, based on pairwise SH added - fflush added to utree output. 5.1.rc2 06.09.2002 - likelihood mapping: simplex labels moved to upper triangle, removed at lower right triangle 5.1.rc1 02.09.2002 - first release candidate for tree-puzzle 5.1 - Changes to the LaTeX manual. CODE FREEZE =========== 5.0.pl30 02.09.2002 - usertree CR bug changed, now accepts trees also in Mac and DOS format (CR or CR+LF). - Q-Support not used in this release (set to FALSE) 5.0.pl29 01.09.2002 - comment added, obsolete/unused functions removed 5.0.pl28 30.08.2002 - Version-no./Copyright changed in the file headers 5.0.pl27 29.08.2002 - Quartet support for inner edges added. Q-Support is computed and added to consensus tree. [todo: Q-Support output in final tree (fputphylogeny)] 5.0.pl26 15.08.2002 - Changes for CodeWarrior added (thanx to Andrew) 5.0.pl25 05.08.2002 - Ambiguous Characters Statistics changed: sum added 5.0.pl24 17.05.2002 - Quartet statistics changed; badqs and badtaxon removed 5.0.pl23 17.05.2002 - find all congruent splits below 50% - output congruent splits below 50% to puzzle file 5.0.pl22 16.05.2002 - cmdline flag '-sub50' added: computation of consensus with splits below 50%, until incongruence or ambiguity 5.0.pl21 13.05.2002 - badtaxon moved from ml.h to puzzle.h and ... - quartet statistics extended from to unresoved (bad) quartets to also fully and partly resolved quartets. - TODO: remove badqs and badtaxon from sources obsolete by fullresqs, partresqs, unresqs, qinfomatr 5.0.pl20 07.05.2002 - a few comments added - '\0' delimited species name array Namestr added for better access. Copied from undelimited Identif after read in. - check for name match while reading in quartets added. exit if mismatch. 5.0.pl19 07.05.2002 - gaps and ambiguous characters added to puzzle report - abort when ambiguous characters = 100% - warning removed from translatedataset, because it ambiguity depends on datatype - might change in menu 5.0.pl18 03.04.2002 - src/test* removed from configure.ac and source tree 5.0.pl17 26.03.2002 - fflush added to evaluatetree after printing tree to treefile 5.0.pl16 20.03.2002 - files adapted for CVS (Id tag added to files) - manual converted from HTML to LaTeX, pdflatex added to Makefile.am 5.0.pl15 19.03.2002 - parameters added (translatedatas,getseqs,getdataset) - all malloc substituted by calloc. 5.0.pl14 15.03.2002 - counting gaps and ambiguous characters in sequence. print warning if > 50 percent. 5.0.pl13 29.02.2002 - exchange O(n^2) chooser by one using O(n) - ml3.c renamed to mlparam.c to collect routines for parameter estimation. - estimateparametersnotree, estimateparameterstree moved to mlparam.c/ml.h - optimseqevolparamsq/optimseqevolparamst renamed to optimseqevolparamsquart/optimseqevolparamstree 5.0.pl12 20.12.2001 - migration to automake 1.5/autoconf 2.52-minor changes - configure changed to use src/config.h - $(srcdir) added to allow build in other directories 5.0.pl11 19.12.2001 - alignment input fixed to accept also Mac format (CR) - removed debug message from 5.0.pl10 - dependencies on Makefile added 5.0.pl10 18.12.2001 - root root search bug, the kept root fixed after first root search. Was introduced in 5.0.pl5. 5.0.pl9 18.12.2001 - possible number of charcters per node in tree strings enlarged from 23/2 to 50. CHAR_PER_TREENODE introduced - typo basian, fixed to Bayesian 5.0.pl8 18.12.2001 - added parameter -achim - fixed doubly opened treefile - adopted to new autoconf/automake (e.g. EXEEXT added) 5.0.pl7 14.11.2001 - computation of rate categories moved to appropriate place in workflow. in some cases categories were computed without likelihoods from tree ready. consequently the output RATE HETEROGENEITY parameter had to move further to the end. - comments added to code - cc added to MPICC (CRAY MPI compiler) 5.0.pl6 20.08.2001 - inputfile name output in the puzzle report for interactive case corrected. was: infile 5.0.pl5 18.08.2001 - minor clock bug corrected, that set the location of the clocked root to first sequence. 5.0.pl4 19.07.2001 - VT matrix corrected, printratematrix added - minor compile time warnings fixed 5.0.pl3 05.07.2001 - radixsort renamed to tp_radixsort to avoid name clashes on Mac OS X - manual replaced by corrected version 5.0.pl2 09.01.2001 - LIBS moved to the end of the linker statement in the Makefile 5.0.pl1 15.11.2000 - Maxspc casted to double for log10 - 200% bug fixed by adding fabs(), log-likelihood differences should not become negative 5.0 26.08.2000 - changes to manual, Makefile.in - cpREV hidden by -DCPREV flag - chi2test, quartio included into source code files - generic scr/Makefile.generic - src/makefile.com for VAX - AUTHORS, README, ChangeLog updated - INSTALL checked 27.08.2000 - test code excluded - '-randseed#' added for debugging purposes - ./data added to autoconf/automake - warning output if cmdline parameter unknown 11.10.2000 - fixed output of rate categories of sites before computing them - check whether rate categories were computed by 1st user tree or NJ tree fixed in the output 12.10.2000 - invariant site model normalization fixed CODE FREEZE =========== 5.0.a33 15.08.2000 - changes for autoconf/automake 5.0.a32 01.08.2000 - a FPE error fixed (badq == 0) - small error in -bestq fixed - fflush's added at several places 5.0.a31 01.08.2000 - comments added to tree structure sorting puzzle2.c - changes in configure.in, Makefile.in 5.0.a30 23.07.2000 - some debugging in checkquart - changed to autoconf 5.0.a29 13.07.2000 - some debugging in checkquart 5.0.a28 13.07.2000 - use best quartet topology option (-bestq) implemented 5.0.a27 13.07.2000 - further developement to checkquart - ascii/binary quartet values (-wqla/-wqlb) - typo correction 5.0.a26 11.07.2000 - fflush at all checktimer - further developement at checkquart - possibility to write quartet values to file (-wqlh) 5.0.a25 06.07.2000 - fflush at checktimer 5.0.a24 02.07.2000 - further debugging of checkquart 5.0.a23 02.07.2000 - further developement to checkquart 5.0.a22 29.06.2000 - checkquart added to makefile - bad quartet stats added after reading in *.allquarts 5.0.a21 27.06.2000 - site pattern statistics implemented and added to SEQUENCE ALIGNMENT section in puzzle report 5.0.a20 26.06.2000 - cpREV45 implemented 5.0.a19 26.06.2000 - for debugging purposes: typo "MPE" changed to "FPE" - fflush(stdout) added in chi2test 5.0.a18 20.06.2000 - checkquart implemented 5.0.a17 19.06.2000 - FPRINTF(STDOUTFILE and STDOUT definition changed and moved; fputid/fputid10 writes to STDOUT instead of stdout - ppuzzle checks slaves enough slave-processes - numquarts, num2quart, quart2num moved from ppuzzle.c to puzzle1.c - read/writeallquart implemented (undocumented feature) to be used by -wqf/-rqf at comandline -wqf = write quartet file (infilename.allquart) after quartet evaluation -rqf = read quartet file (infilename.allquart), no quartet evaluation, unless -wqf is used as well, then quartets are written and read in - '-h' option at comandline -> printusage 5.0.a16 31.05.2000 - chi2test bug fixed - WAG matrix added, model choice adopted 13.06.2000 - date set to June 2000 - author order changed to Schmidt, Strimmer, Vingron, v.Haeseler - CPU time output stopped, due to overflow errors 16.06.2000 - sequence composition chi2test moved before parameter output. - output of chi2test and bad quartet statistics split, to do the chi2test output earlier. 5.0.a15 02.05.2000 - Names changed back from TREE-PUZZLE to PUZZLE 09.05.2000 - and to TREE-PUZZLE again ;-) 5.0.a14 13.03.2000 - Changes to the manual. - Executable names changed to (p)treepuzzle. (changes in the makefiles) 15.03.2000 - Output of parameters after estimation added. 5.0.a13 18.02.2000 - ALPHA version number removed from the code 5.0.a12 18.02.2000 - CPU time measurement problems fixed for case where clock_t is an unsigned type. 5.0.a11 17.02.2000 - time measure problems (CPU/wallclock) fixed not all features in addtimes are used at the moment. - unnecessary and unused routines removed fron source code. 5.0.a10 20.01.2000 - Name changes from PUZZLE to TREE-PUZZLE - Chi2-fit model guessing for VT model added - little model printing bug fixed 5.0.a9 22.12.1999 - VT Model incorporated (Mueller, Vingron (2000) JCB, to appear). - TODO: Chi2-fit model guessing for VT model 5.0.a8 21.12.1999 - 'sys/times.h' and 'sys/types.h' removed from puzzle.h. They were neither ANSI conform nor necessary, but occured in the SUN man pages. - Definition and call of writetimesstat eliminated from the sequention version by compiler switched, and not just the function body as before. - '-O4' canged to '-O' to be more generic. 5.0.a7 21.12.1999 - Macro constants introduced for data_optn (NUCLEOTIDE, AMINOACID, BINARY) - round robbing of datatype and AA model option changed in menu to make adjustment of the model possible by a determined sequence of letters: 'd': Auto -> Nucleotides -> Amino acids -> Binary states -> Auto ('m' && data_optn == AMINOACID): Auto -> Dayhoff -> JTT -> mtREV24 -> BLOSUM62 -> Auto - manual.html adjusted 5.0.a6 20.12.1999 - new manual.html added 5.0.a5 07.12.1999 - output bug fixed (bestrates were written before they were computed) 5.0.a4 02.12.1999 - header file inclusion ajusted: added: #include changed from: #include "ppuzzle.h" to: #ifdef PARALLEL # include "ppuzzle.h" #endif 5.0.a3 27.11.1999 - '-h' comandline option removed, because of problems with MPICH under LINUX - new memory leaks of 5.0.a2 closed in PP_Finalize 5.0.a2 27.11.1999 - Cleanup of the source code - Measurement of CPU time added - Parallel load statistics added (quartets, trees, time) to puzzle report. - Cleanup debug messages - Comments "[...]" are removed from usertrees now. - single quotes will only be printed arount species names if -DUSEQUOTES is set at compiletime. - tree likelihood is printed infront of a tree as a comment, [ lh=-xx.xxxxx ](...); 5.0.a1 26.11.1999 - Cleanup of the directories - Copyright changes - Version changes VERSION CHANGE ============== 4.1.a26 25.11.1999 - Makefile made universal for pauzzle and ppuzzle - lines not needed removed from puzzle.h 4.1.a25 19.11.1999 - Output file prefixes for distances, trees, and puzzlereport changed in user trees analysis case to user tree file name - Temporary output of likelihood to treefile added 4.1.a24 11.11.1999 - Output of puzzling step trees changed ptorder: [ orderno # % ID #UniqTopos #Steps ]PHYLIP pstep: chunk #InChunk sum ID #UniqTopos #Steps - preliminary leap frog RNG implemented, i.e. uses the rand4 in the usual way in the sequential case. If run in parallel all rand4 are initialized with the same seed and started with PP_Myid-th random number. after that each process uses the every PP_NumProcs-th random number to make sure that these unique. 4.1.a23 08.11.1999 - output of sequential and parallel version to *.pstep made identical 4.1.a22 05.11.1999 - two different puzzle step tree outputs intruduced and added to the menu ("[ 1. 35 ](...);": - ordered unique tree list -> *.ptorder Format: "[ 1. 35 ]" (Ordernumber, Amount) - chronological tree list -> *.pstep Format: "[ 1. 35 ]" (Chunknumber, Amount in chunk) (the last is a problem in parallel, because the come in chunks, as scheduled) - debugged the output 4.1.a21 04.11.1999 - Makefile adjustments for other Plattforms - pstep tree output changed. unique treestructures printed to *.pstep file with a leading comment containing an order number and the ammount padded with blanks (e.g. "[ 1. 356 ]('mouse'..."). output is done right before writing the puzzle file. - controlled MPI finish to the Quit menu option added 4.1.a20 03.11.1999 - some garbage collection (free) added - makefile adjusted, OFLAGS for optimization added (ppuzzle/MPICH has problems with -O, so the ppuzzle is created without optimization) Some minor changes in the makefiles - still to do: garbage collection from 'internalnode' in master process 4.1.a19 13.10.1999 - adding the output of standardized (i.e. sorted) puzzling step trees. Those are printed to the standard output at the moment. (Routines to sort and print the trees implemented) 14.10.1999 - routines for printing the sorted trees to a string. needed to send them between Master and Worker, and to have a unique key to sort and count the trees. 21.10.1999 - counting of sorted trees implemented by doubly linked list, sort routine, print to stdout 25.10.1999 - change place of writing distances to file right after distances have been computed. - output of puzzling step trees now with true name, not numbers 02.11.1999 - parallel counting and sending of puzzling step trees - some parallel sending bugs fixed 4.1.a18 14.09.1999 - adding possibility to specify input file at command line, this specifies also the output filenames (puzzle output: *.puzzle; treefile: *.tree; distances: *.dist; Triangel EPS: *.eps; unresolved: *.qlist; puzzling step trees: *.pstep) If an unexisting name is given, one has to reenter the right name, but the wrong one is used as prefix. 15.09.1999 - sending back of bad quartets from slaves added - bug in quart2num fixed (not used before; was shifted by 1) - first version of a README added ;-) 4.1.a17 03.08.1999 - Recv-Error in receiving DoPuzzleBlock fixed - double freeing of same MPI_Datatype fixed - changing of scheduling algorithm to smaller chunks in gss -> sgss 13.09.1999 - bug fixed in optimization routine in ml2.c: boundary check added 4.1.a16 12.07.1999 - slight changes in verbosity levels - changed all printf to FPRINTF(STDOUTFILE to change easily from stdout to a file. 4.1.a15 08.07.1999 - scheduler for both parallel parts - several small changes 4.1.a14 25.06.1999 - computation of tree parallel, scheduler dependent, sending all biparts in one message instead of one by one - several small changes since a13 in sched.c, et al. 4.1.a13 10.06.1999 - computation of tree parallel (chunk = #trees/#slaves) - scheduling schemes implemented for minimum chunk sizes 4.1.a12 07.06.1999 - computation of quartets properly parallel - scheduling implemented - counting of quartets by slave ajusted - TODO: sending of bad quartets (array + list) - distinction between '1st user tree' and 'NJ tree' in result output removed again 4.1.a11 28.05.1999 - PP_SendDoQuartBlock, PP_RecvDoQuartBlock, PP_SendQuartBlock, PP_RecvQuartBlock - mallocquartets() changed from global to local variables to be more flexible - Quartet computation moved to slave (badquartet handling missing: output, badquartet vector); - distinction between '1st user tree' and 'NJ tree' added in result output (puzzle1.c around l.1756) 4.1.a10 20.05.1999 - num2quart, numquarts, quart2num introduced - parallel init/finalize, quartets computed on master and slave, compared -> equal -> all necessary parameter exported 4.1.a9 19.05.1999 - 'dvector forg' removed from onepamratematrix cmdline, because it's not used in the function. 4.1.a8 18.05.1999 - add _GAMMA_ (not necessary) to gamma.h and _PUZZLE_ to puzzle.h to avoid dublicate includes, possible due to ppuzzle.h - ppuzzle added to makefile and to check - 1st parallel version but no slave computations only sending parameters and done signals. 4.1.a7 18.05.1999 - export reevaluation of tree and evaluation of usertrees to evaluatetree. 4.1.a6 17.05.1999 - -DNEWFORLOOP added to fixed.src, because the changed for loop structure changes the sequence of randomized quartets during likelihood mapping - change 'int main()' to 'int main(argc, argv)' - export more functionalities from main: memcleanup(), inputandinit(&argc, &argv) - grouping if's (excluding eachother) together in switch() - split treereavaluation and 1st usertree, evaluate all usertrees together (TODO: both, treereavaluation and usertrees in one loop) - MAKE CHECK added to ./makefile 4.1.a5 16.05.1999 - adding dvector Brnlength to lslength cmdline to reduce globality of Brnlength. (Later better to *Tree) 4.1.a4 11.05.1999 - structure of for loops changed in computeallquartets and recon_tree, so that the quarted addresses are in one contigous sequence (for a Copyright (C) This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Also add information on how to contact you by electronic and paper mail. If the program is interactive, make it output a short notice like this when it starts in an interactive mode: Gnomovision version 69, Copyright (C) year name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program. You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the program, if necessary. Here is a sample; alter the names: Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (which makes passes at compilers) written by James Hacker. , 1 April 1989 Ty Coon, President of Vice This General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Library General Public License instead of this License.