diff options
Diffstat (limited to 'academic/PhyML/20131112.patch')
| -rw-r--r-- | academic/PhyML/20131112.patch | 1591 |
1 files changed, 1591 insertions, 0 deletions
diff --git a/academic/PhyML/20131112.patch b/academic/PhyML/20131112.patch new file mode 100644 index 0000000000..e7eb2670b6 --- /dev/null +++ b/academic/PhyML/20131112.patch @@ -0,0 +1,1591 @@ +unchanged: +--- ./phyml-20120412/src/help.c 2011-09-22 14:51:57.000000000 +1200 ++++ ./phyml-20120412-new-bak/src/help.c 2013-02-18 21:51:51.448662440 +1300 +@@ -96,7 +96,7 @@ + PhyML_Printf("\n"); + + +- PhyML_Printf("%s\n\t-q (or --sequential)\n",BOLD); ++ PhyML_Printf("%s\n\t-q (or --sequential)%s\n",BOLD,FLAT); + PhyML_Printf("%s\t\tChanges interleaved format (default) to sequential format.\n",FLAT); + PhyML_Printf("\n"); + +unchanged: +--- ./phyml-20120412/src/lk.c 2012-04-05 14:47:37.000000000 +1200 ++++ ./phyml-20120412-new-bak/src/lk.c 2013-02-19 10:22:22.665284529 +1300 +@@ -472,7 +472,7 @@ + phydbl site_lk_cat, site_lk; + int sum_scale_left, sum_scale_rght; + int fact_sum_scale; +- phydbl max_sum_scale; ++ phydbl max_sum_scale,min_sum_scale; + phydbl sum; + int ambiguity_check,state; + int catg,ns,k,l,site; +@@ -481,11 +481,12 @@ + phydbl multiplier; + int exponent, piecewise_exponent; + phydbl tmp; +- phydbl logbig; ++ phydbl logbig,logsmall; + phydbl inv_site_lk; + + +- logbig = LOG((phydbl)BIG); ++ logbig = LOG((phydbl)BIG); ++ logsmall = LOG((phydbl)SMALL); + + dim1 = tree->mod->n_catg * tree->mod->ns; + dim2 = tree->mod->ns; +@@ -555,7 +556,7 @@ + b->Pij_rr[catg*dim3+k*dim2+l] * + b->p_lk_left[site*dim1+catg*dim2+l]; + } +- ++ + site_lk_cat += + sum * + tree->mod->pi->v[k] * +@@ -578,7 +579,7 @@ + b->Pij_rr[catg*dim3+k*dim2+l] * + b->p_lk_left[site*dim1+catg*dim2+l]; + } +- ++ + site_lk_cat += + sum * + tree->mod->pi->v[k] * +@@ -588,8 +589,9 @@ + } + tree->site_lk_cat[catg] = site_lk_cat; + } +- ++ + max_sum_scale = (phydbl)BIG; ++ min_sum_scale = (phydbl)SMALL; + For(catg,tree->mod->n_catg) + { + sum_scale_left_cat[catg] = +@@ -606,18 +608,30 @@ + + if(sum < .0) + { +- PhyML_Printf("\n. sum = %G",sum); +- PhyML_Printf("\n. Err in file %s at line %d\n\n",__FILE__,__LINE__); ++ PhyML_Printf("\n== sum = %G",sum); ++ PhyML_Printf("\n== Err in file %s at line %d\n\n",__FILE__,__LINE__); + Warn_And_Exit("\n"); + } + + tmp = sum + (logbig - LOG(tree->site_lk_cat[catg]))/(phydbl)LOG2; + if(tmp < max_sum_scale) max_sum_scale = tmp; /* min of the maxs */ ++ ++ tmp = sum + (logsmall - LOG(tree->site_lk_cat[catg]))/(phydbl)LOG2; ++ if(tmp > min_sum_scale) min_sum_scale = tmp; /* max of the mins */ + } + +-/* fact_sum_scale = (int)((max_sum_scale + min_sum_scale) / 2); */ ++ if(min_sum_scale > max_sum_scale) ++ { ++ /* PhyML_Printf("\n== Numerical precision issue alert."); */ ++ /* PhyML_Printf("\n== min_sum_scale = %G max_sum_scale = %G",min_sum_scale,max_sum_scale); */ ++ /* PhyML_Printf("\n== Err in file %s at line %d\n\n",__FILE__,__LINE__); */ ++ /* Warn_And_Exit("\n"); */ ++ min_sum_scale = max_sum_scale; ++ } ++ ++ fact_sum_scale = (int)((max_sum_scale + min_sum_scale) / 2); + +- fact_sum_scale = (int)(max_sum_scale / 2); ++ /* fact_sum_scale = (int)(max_sum_scale / 2); */ + + /* Apply scaling factors */ + For(catg,tree->mod->n_catg) +@@ -651,12 +665,13 @@ + + if(isinf(site_lk_cat)) + { +- PhyML_Printf("\n+ site=%4d cat=%4d site_lk_cat=%G sum_scale=%d max=%G fact=%d expo=%d dbl=%G", ++ PhyML_Printf("\n+ site=%4d cat=%4d site_lk_cat=%G sum_scale=%d max=%G min=%G fact=%d expo=%d dbl=%G", + tree->curr_site, + catg, + tree->site_lk_cat[catg], + sum_scale_left_cat[catg]+sum_scale_rght_cat[catg], + max_sum_scale, ++ min_sum_scale, + fact_sum_scale, + -(sum_scale_left_cat[catg]+sum_scale_rght_cat[catg])+fact_sum_scale, + (double)tree->site_lk_cat[catg] * pow(2.,-(sum_scale_left_cat[catg]+sum_scale_rght_cat[catg])+fact_sum_scale)); +@@ -678,13 +693,11 @@ + fact_sum_scale, + -(sum_scale_left_cat[catg]+sum_scale_rght_cat[catg])+fact_sum_scale, + (double)tree->site_lk_cat[catg] * pow(2.,-(sum_scale_left_cat[catg]+sum_scale_rght_cat[catg])+fact_sum_scale)); +- ++ + Exit("\n"); + } +- + site_lk_cat = .0; + } +- + tree->site_lk_cat[catg] = site_lk_cat; + } + +@@ -694,6 +707,24 @@ + site_lk += tree->site_lk_cat[catg] * tree->mod->gamma_r_proba->v[catg]; + } + ++ if(isinf(site_lk)) ++ { ++ PhyML_Printf("\n= Site = %d",site); ++ PhyML_Printf("\n= invar = %d",tree->data->invar[site]); ++ PhyML_Printf("\n= scale_left = %d scale_rght = %d",sum_scale_left,sum_scale_rght); ++ PhyML_Printf("\n= lk = %G log(lk) = %f < %G",site_lk,log_site_lk,-BIG); ++ PhyML_Printf("\n= fact_sum_scale = %d",fact_sum_scale); ++ For(catg,tree->mod->n_catg) PhyML_Printf("\n. rr=%f p=%f lk=%G expo=%d", ++ tree->mod->gamma_rr->v[catg], ++ tree->mod->gamma_r_proba->v[catg], ++ tree->site_lk_cat[catg], ++ -(sum_scale_left_cat[catg]+sum_scale_rght_cat[catg])+fact_sum_scale); ++ PhyML_Printf("\n= pinv = %G",tree->mod->pinvar->v); ++ PhyML_Printf("\n= bl mult = %G",tree->mod->br_len_multiplier->v); ++ PhyML_Printf("\n. Err in file %s at line %d",__FILE__,__LINE__); ++ Warn_And_Exit("\n"); ++ } ++ + + inv_site_lk = 0.; + +@@ -741,19 +772,22 @@ + + log_site_lk = LOG(site_lk) - (phydbl)LOG2 * fact_sum_scale; + +- + For(catg,tree->mod->n_catg) tree->log_site_lk_cat[catg][site] = LOG(tree->site_lk_cat[catg]) - (phydbl)LOG2 * fact_sum_scale; + + if(isinf(log_site_lk) || isnan(log_site_lk)) + { +- PhyML_Printf("\n. Site = %d",site); +- PhyML_Printf("\n. invar = %d",tree->data->invar[site]); +- PhyML_Printf("\n. scale_left = %d scale_rght = %d",sum_scale_left,sum_scale_rght); +- PhyML_Printf("\n. inv_site_lk = %f",inv_site_lk); +- PhyML_Printf("\n. Lk = %G LOG(Lk) = %f < %G",site_lk,log_site_lk,-BIG); +- For(catg,tree->mod->n_catg) PhyML_Printf("\n. rr=%f p=%f",tree->mod->gamma_rr->v[catg],tree->mod->gamma_r_proba->v[catg]); +- PhyML_Printf("\n. pinv = %G",tree->mod->pinvar->v); +- PhyML_Printf("\n. bl mult = %G",tree->mod->br_len_multiplier->v); ++ PhyML_Printf("\n= Site = %d",site); ++ PhyML_Printf("\n= invar = %d",tree->data->invar[site]); ++ PhyML_Printf("\n= scale_left = %d scale_rght = %d",sum_scale_left,sum_scale_rght); ++ PhyML_Printf("\n= inv_site_lk = %f",inv_site_lk); ++ PhyML_Printf("\n= lk = %G log(lk) = %f < %G",site_lk,log_site_lk,-BIG); ++ For(catg,tree->mod->n_catg) PhyML_Printf("\n. rr=%f p=%f lk=%G", ++ tree->mod->gamma_rr->v[catg], ++ tree->mod->gamma_r_proba->v[catg], ++ tree->site_lk_cat[catg]); ++ PhyML_Printf("\n= pinv = %G",tree->mod->pinvar->v); ++ PhyML_Printf("\n= bl mult = %G",tree->mod->br_len_multiplier->v); ++ PhyML_Printf("\n= fact_sum_scale = %d",fact_sum_scale); + + /* int i; */ + /* For(i,2*tree->n_otu-3) */ +@@ -802,6 +836,7 @@ + Alias_One_Subpatt((d==b->left)?(b->rght):(b->left),d,tree); + + if(d->tax) return; ++ + + if(tree->mod->use_m4mod == NO) + { +@@ -813,6 +848,10 @@ + { + Update_P_Lk_AA(tree,b,d); + } ++ else ++ { ++ Update_P_Lk_Generic(tree,b,d); ++ } + } + else + { +@@ -1044,7 +1083,7 @@ + + p_lk[site*NsNg+catg*Ns+i] = p1_lk1 * p2_lk2; + +- /* PhyML_Printf("\n+ %G",p_lk[site*NsNg+catg*Ns+i]); */ ++ /* PhyML_Printf("\n+ %G",p_lk[site*NsNg+catg*Ns+i]); */ + + if(p_lk[site*NsNg+catg*Ns+i] < smallest_p_lk) smallest_p_lk = p_lk[site*NsNg+catg*Ns+i] ; + } +unchanged: +--- ./phyml-20120412/src/Makefile 1970-01-01 12:00:00.000000000 +1200 ++++ ./phyml-20120412-new-bak/src/Makefile 2013-02-18 21:54:46.957806553 +1300 +@@ -0,0 +1,1082 @@ ++# Makefile.in generated by automake 1.11.1 from Makefile.am. ++# src/Makefile. Generated from Makefile.in by configure. ++ ++# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, ++# 2003, 2004, 2005, 2006, 2007, 2008, 2009 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. ++ ++ ++ ++ ++pkgdatadir = $(datadir)/phyml ++pkgincludedir = $(includedir)/phyml ++pkglibdir = $(libdir)/phyml ++pkglibexecdir = $(libexecdir)/phyml ++am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd ++install_sh_DATA = $(install_sh) -c -m 644 ++install_sh_PROGRAM = $(install_sh) -c ++install_sh_SCRIPT = $(install_sh) -c ++INSTALL_HEADER = $(INSTALL_DATA) ++transform = $(program_transform_name) ++NORMAL_INSTALL = : ++PRE_INSTALL = : ++POST_INSTALL = : ++NORMAL_UNINSTALL = : ++PRE_UNINSTALL = : ++POST_UNINSTALL = : ++build_triplet = x86_64-unknown-linux-gnu ++host_triplet = x86_64-unknown-linux-gnu ++bin_PROGRAMS = phyml$(EXEEXT) ++#bin_PROGRAMS = test$(EXEEXT) ++#bin_PROGRAMS = phyml-mpi$(EXEEXT) ++#bin_PROGRAMS = rf$(EXEEXT) ++#bin_PROGRAMS = m4$(EXEEXT) ++#bin_PROGRAMS = tiporder$(EXEEXT) ++#bin_PROGRAMS = part$(EXEEXT) ++#bin_PROGRAMS = \ ++# phycont$(EXEEXT) ++#bin_PROGRAMS = phytime$(EXEEXT) ++subdir = src ++DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in ++ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 ++am__aclocal_m4_deps = $(top_srcdir)/configure.ac ++am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ ++ $(ACLOCAL_M4) ++mkinstalldirs = $(install_sh) -d ++CONFIG_HEADER = $(top_builddir)/config.h ++CONFIG_CLEAN_FILES = ++CONFIG_CLEAN_VPATH_FILES = ++am__installdirs = "$(DESTDIR)$(bindir)" ++PROGRAMS = $(bin_PROGRAMS) ++am__m4_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \ ++ optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \ ++ free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \ ++ pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h mg.c \ ++ mg.h times.c times.h mcmc.c mcmc.h rates.c rates.h spr.c spr.h \ ++ draw.c draw.h stats.c stats.h tiporder.c tiporder.h m4.c m4.h ++#am_m4_OBJECTS = main.$(OBJEXT) \ ++# utilities.$(OBJEXT) \ ++# optimiz.$(OBJEXT) \ ++# lk.$(OBJEXT) \ ++# bionj.$(OBJEXT) \ ++# models.$(OBJEXT) \ ++# free.$(OBJEXT) \ ++# help.$(OBJEXT) \ ++# simu.$(OBJEXT) \ ++# eigen.$(OBJEXT) \ ++# pars.$(OBJEXT) \ ++# alrt.$(OBJEXT) \ ++# interface.$(OBJEXT) \ ++# cl.$(OBJEXT) \ ++# mg.$(OBJEXT) \ ++# times.$(OBJEXT) \ ++# mcmc.$(OBJEXT) \ ++# rates.$(OBJEXT) \ ++# spr.$(OBJEXT) \ ++# draw.$(OBJEXT) \ ++# stats.$(OBJEXT) \ ++# tiporder.$(OBJEXT) \ ++# m4.$(OBJEXT) ++m4_OBJECTS = $(am_m4_OBJECTS) ++m4_DEPENDENCIES = ++am__part_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \ ++ optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \ ++ free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \ ++ pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h mg.c \ ++ mg.h spr.c spr.h m4.c m4.h draw.c draw.h stats.c stats.h \ ++ tiporder.c tiporder.h ++#am_part_OBJECTS = main.$(OBJEXT) \ ++# utilities.$(OBJEXT) \ ++# optimiz.$(OBJEXT) \ ++# lk.$(OBJEXT) \ ++# bionj.$(OBJEXT) \ ++# models.$(OBJEXT) \ ++# free.$(OBJEXT) \ ++# help.$(OBJEXT) \ ++# simu.$(OBJEXT) \ ++# eigen.$(OBJEXT) \ ++# pars.$(OBJEXT) \ ++# alrt.$(OBJEXT) \ ++# interface.$(OBJEXT) \ ++# cl.$(OBJEXT) \ ++# mg.$(OBJEXT) \ ++# spr.$(OBJEXT) \ ++# m4.$(OBJEXT) \ ++# draw.$(OBJEXT) \ ++# stats.$(OBJEXT) \ ++# tiporder.$(OBJEXT) ++part_OBJECTS = $(am_part_OBJECTS) ++part_DEPENDENCIES = ++am__phycont_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \ ++ optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \ ++ free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \ ++ pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h spr.c \ ++ spr.h times.c times.h m4.c m4.h draw.c draw.h rates.c rates.h \ ++ mcmc.c mcmc.h stats.c stats.h mg.c mg.h tiporder.c tiporder.h ++#am_phycont_OBJECTS = \ ++# main.$(OBJEXT) \ ++# utilities.$(OBJEXT) \ ++# optimiz.$(OBJEXT) \ ++# lk.$(OBJEXT) \ ++# bionj.$(OBJEXT) \ ++# models.$(OBJEXT) \ ++# free.$(OBJEXT) \ ++# help.$(OBJEXT) \ ++# simu.$(OBJEXT) \ ++# eigen.$(OBJEXT) \ ++# pars.$(OBJEXT) \ ++# alrt.$(OBJEXT) \ ++# interface.$(OBJEXT) \ ++# cl.$(OBJEXT) \ ++# spr.$(OBJEXT) \ ++# times.$(OBJEXT) \ ++# m4.$(OBJEXT) \ ++# draw.$(OBJEXT) \ ++# rates.$(OBJEXT) \ ++# mcmc.$(OBJEXT) \ ++# stats.$(OBJEXT) \ ++# mg.$(OBJEXT) \ ++# tiporder.$(OBJEXT) ++phycont_OBJECTS = $(am_phycont_OBJECTS) ++phycont_DEPENDENCIES = ++am__phyml_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \ ++ optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \ ++ free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \ ++ pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h spr.c \ ++ spr.h draw.c draw.h stats.c stats.h rates.c rates.h mcmc.c \ ++ mcmc.h times.c times.h tiporder.c tiporder.h mg.c mg.h m4.c \ ++ m4.h ++am_phyml_OBJECTS = main.$(OBJEXT) \ ++ utilities.$(OBJEXT) \ ++ optimiz.$(OBJEXT) \ ++ lk.$(OBJEXT) \ ++ bionj.$(OBJEXT) \ ++ models.$(OBJEXT) \ ++ free.$(OBJEXT) \ ++ help.$(OBJEXT) \ ++ simu.$(OBJEXT) \ ++ eigen.$(OBJEXT) \ ++ pars.$(OBJEXT) \ ++ alrt.$(OBJEXT) \ ++ interface.$(OBJEXT) \ ++ cl.$(OBJEXT) \ ++ spr.$(OBJEXT) \ ++ draw.$(OBJEXT) \ ++ stats.$(OBJEXT) \ ++ rates.$(OBJEXT) \ ++ mcmc.$(OBJEXT) \ ++ times.$(OBJEXT) \ ++ tiporder.$(OBJEXT) \ ++ mg.$(OBJEXT) \ ++ m4.$(OBJEXT) ++phyml_OBJECTS = $(am_phyml_OBJECTS) ++phyml_DEPENDENCIES = ++am__phyml_mpi_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \ ++ optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \ ++ free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \ ++ pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h spr.c \ ++ spr.h draw.c draw.h mpi_boot.c mpi_boot.h stats.c stats.h \ ++ rates.c rates.h mcmc.c mcmc.h times.c times.h tiporder.c \ ++ tiporder.h mg.c mg.h m4.c m4.h xml.c xml.h ++#am_phyml_mpi_OBJECTS = main.$(OBJEXT) \ ++# utilities.$(OBJEXT) \ ++# optimiz.$(OBJEXT) \ ++# lk.$(OBJEXT) \ ++# bionj.$(OBJEXT) \ ++# models.$(OBJEXT) \ ++# free.$(OBJEXT) \ ++# help.$(OBJEXT) \ ++# simu.$(OBJEXT) \ ++# eigen.$(OBJEXT) \ ++# pars.$(OBJEXT) \ ++# alrt.$(OBJEXT) \ ++# interface.$(OBJEXT) \ ++# cl.$(OBJEXT) \ ++# spr.$(OBJEXT) \ ++# draw.$(OBJEXT) \ ++# mpi_boot.$(OBJEXT) \ ++# stats.$(OBJEXT) \ ++# rates.$(OBJEXT) \ ++# mcmc.$(OBJEXT) \ ++# times.$(OBJEXT) \ ++# tiporder.$(OBJEXT) \ ++# mg.$(OBJEXT) \ ++# m4.$(OBJEXT) \ ++# xml.$(OBJEXT) ++phyml_mpi_OBJECTS = $(am_phyml_mpi_OBJECTS) ++phyml_mpi_DEPENDENCIES = ++am__phytime_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \ ++ optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \ ++ free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \ ++ pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h spr.c \ ++ spr.h times.c times.h m4.c m4.h draw.c draw.h rates.c rates.h \ ++ mcmc.c mcmc.h stats.c stats.h mg.c mg.h tiporder.c tiporder.h ++#am_phytime_OBJECTS = main.$(OBJEXT) \ ++# utilities.$(OBJEXT) optimiz.$(OBJEXT) \ ++# lk.$(OBJEXT) bionj.$(OBJEXT) \ ++# models.$(OBJEXT) free.$(OBJEXT) \ ++# help.$(OBJEXT) simu.$(OBJEXT) \ ++# eigen.$(OBJEXT) pars.$(OBJEXT) \ ++# alrt.$(OBJEXT) interface.$(OBJEXT) \ ++# cl.$(OBJEXT) spr.$(OBJEXT) times.$(OBJEXT) \ ++# m4.$(OBJEXT) draw.$(OBJEXT) rates.$(OBJEXT) \ ++# mcmc.$(OBJEXT) stats.$(OBJEXT) mg.$(OBJEXT) \ ++# tiporder.$(OBJEXT) ++phytime_OBJECTS = $(am_phytime_OBJECTS) ++phytime_DEPENDENCIES = ++am__rf_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \ ++ optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \ ++ free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \ ++ pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h mg.c \ ++ mg.h times.c times.h mcmc.c mcmc.h rates.c rates.h spr.c spr.h \ ++ draw.c draw.h stats.c stats.h tiporder.c tiporder.h m4.c m4.h ++#am_rf_OBJECTS = main.$(OBJEXT) \ ++# utilities.$(OBJEXT) \ ++# optimiz.$(OBJEXT) \ ++# lk.$(OBJEXT) \ ++# bionj.$(OBJEXT) \ ++# models.$(OBJEXT) \ ++# free.$(OBJEXT) \ ++# help.$(OBJEXT) \ ++# simu.$(OBJEXT) \ ++# eigen.$(OBJEXT) \ ++# pars.$(OBJEXT) \ ++# alrt.$(OBJEXT) \ ++# interface.$(OBJEXT) \ ++# cl.$(OBJEXT) \ ++# mg.$(OBJEXT) \ ++# times.$(OBJEXT) \ ++# mcmc.$(OBJEXT) \ ++# rates.$(OBJEXT) \ ++# spr.$(OBJEXT) \ ++# draw.$(OBJEXT) \ ++# stats.$(OBJEXT) \ ++# tiporder.$(OBJEXT) \ ++# m4.$(OBJEXT) ++rf_OBJECTS = $(am_rf_OBJECTS) ++rf_DEPENDENCIES = ++am__test_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \ ++ optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \ ++ free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \ ++ pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h spr.c \ ++ spr.h draw.c draw.h stats.c stats.h rates.c rates.h mcmc.c \ ++ mcmc.h times.c times.h tiporder.c tiporder.h mg.c mg.h m4.c \ ++ m4.h xml.c xml.h ++#am_test_OBJECTS = main.$(OBJEXT) \ ++# utilities.$(OBJEXT) \ ++# optimiz.$(OBJEXT) \ ++# lk.$(OBJEXT) \ ++# bionj.$(OBJEXT) \ ++# models.$(OBJEXT) \ ++# free.$(OBJEXT) \ ++# help.$(OBJEXT) \ ++# simu.$(OBJEXT) \ ++# eigen.$(OBJEXT) \ ++# pars.$(OBJEXT) \ ++# alrt.$(OBJEXT) \ ++# interface.$(OBJEXT) \ ++# cl.$(OBJEXT) \ ++# spr.$(OBJEXT) \ ++# draw.$(OBJEXT) \ ++# stats.$(OBJEXT) \ ++# rates.$(OBJEXT) \ ++# mcmc.$(OBJEXT) \ ++# times.$(OBJEXT) \ ++# tiporder.$(OBJEXT) \ ++# mg.$(OBJEXT) \ ++# m4.$(OBJEXT) \ ++# xml.$(OBJEXT) ++test_OBJECTS = $(am_test_OBJECTS) ++test_DEPENDENCIES = ++am__tiporder_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \ ++ optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \ ++ free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \ ++ pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h mg.c \ ++ mg.h times.c times.h mcmc.c mcmc.h rates.c rates.h spr.c spr.h \ ++ m4.c m4.h draw.c draw.h stats.c stats.h tiporder.c tiporder.h ++#am_tiporder_OBJECTS = main.$(OBJEXT) \ ++# utilities.$(OBJEXT) \ ++# optimiz.$(OBJEXT) \ ++# lk.$(OBJEXT) \ ++# bionj.$(OBJEXT) \ ++# models.$(OBJEXT) \ ++# free.$(OBJEXT) \ ++# help.$(OBJEXT) \ ++# simu.$(OBJEXT) \ ++# eigen.$(OBJEXT) \ ++# pars.$(OBJEXT) \ ++# alrt.$(OBJEXT) \ ++# interface.$(OBJEXT) \ ++# cl.$(OBJEXT) \ ++# mg.$(OBJEXT) \ ++# times.$(OBJEXT) \ ++# mcmc.$(OBJEXT) \ ++# rates.$(OBJEXT) \ ++# spr.$(OBJEXT) \ ++# m4.$(OBJEXT) \ ++# draw.$(OBJEXT) \ ++# stats.$(OBJEXT) \ ++# tiporder.$(OBJEXT) ++tiporder_OBJECTS = $(am_tiporder_OBJECTS) ++tiporder_DEPENDENCIES = ++DEFAULT_INCLUDES = -I. -I$(top_builddir) ++depcomp = $(SHELL) $(top_srcdir)/depcomp ++am__depfiles_maybe = depfiles ++am__mv = mv -f ++COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ ++ $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) ++AM_V_CC = $(am__v_CC_$(V)) ++am__v_CC_ = $(am__v_CC_$(AM_DEFAULT_VERBOSITY)) ++am__v_CC_0 = @echo " CC " $@; ++AM_V_at = $(am__v_at_$(V)) ++am__v_at_ = $(am__v_at_$(AM_DEFAULT_VERBOSITY)) ++am__v_at_0 = @ ++CCLD = $(CC) ++LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@ ++AM_V_CCLD = $(am__v_CCLD_$(V)) ++am__v_CCLD_ = $(am__v_CCLD_$(AM_DEFAULT_VERBOSITY)) ++am__v_CCLD_0 = @echo " CCLD " $@; ++AM_V_GEN = $(am__v_GEN_$(V)) ++am__v_GEN_ = $(am__v_GEN_$(AM_DEFAULT_VERBOSITY)) ++am__v_GEN_0 = @echo " GEN " $@; ++SOURCES = $(m4_SOURCES) $(part_SOURCES) $(phycont_SOURCES) \ ++ $(phyml_SOURCES) $(phyml_mpi_SOURCES) $(phytime_SOURCES) \ ++ $(rf_SOURCES) $(test_SOURCES) $(tiporder_SOURCES) ++DIST_SOURCES = $(am__m4_SOURCES_DIST) $(am__part_SOURCES_DIST) \ ++ $(am__phycont_SOURCES_DIST) $(am__phyml_SOURCES_DIST) \ ++ $(am__phyml_mpi_SOURCES_DIST) $(am__phytime_SOURCES_DIST) \ ++ $(am__rf_SOURCES_DIST) $(am__test_SOURCES_DIST) \ ++ $(am__tiporder_SOURCES_DIST) ++ETAGS = etags ++CTAGS = ctags ++DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST) ++ACLOCAL = ${SHELL} /home/guindon/Downloads/phyml-20120412/missing --run aclocal-1.11 ++AMTAR = ${SHELL} /home/guindon/Downloads/phyml-20120412/missing --run tar ++AM_DEFAULT_VERBOSITY = 1 ++AUTOCONF = ${SHELL} /home/guindon/Downloads/phyml-20120412/missing --run autoconf ++AUTOHEADER = ${SHELL} /home/guindon/Downloads/phyml-20120412/missing --run autoheader ++AUTOMAKE = ${SHELL} /home/guindon/Downloads/phyml-20120412/missing --run automake-1.11 ++AWK = gawk ++CC = gcc ++CCDEPMODE = depmode=gcc3 ++CFLAGS = -ansi -pedantic -Wall -std=c99 -O0 -g ++CPP = gcc -E ++CPPFLAGS = ++CYGPATH_W = echo ++DEFS = $(REVISION) ++DEPDIR = .deps ++ECHO_C = ++ECHO_N = -n ++ECHO_T = ++EGREP = /usr/bin/grep -E ++EXEEXT = ++GREP = /usr/bin/grep ++INSTALL = /usr/bin/install -c ++INSTALL_DATA = ${INSTALL} -m 644 ++INSTALL_PROGRAM = ${INSTALL} ++INSTALL_SCRIPT = ${INSTALL} ++INSTALL_STRIP_PROGRAM = $(install_sh) -c -s ++LDFLAGS = ++LIBOBJS = ++LIBS = -lm ++LTLIBOBJS = ++MAKEINFO = ${SHELL} /home/guindon/Downloads/phyml-20120412/missing --run makeinfo ++MKDIR_P = /usr/bin/mkdir -p ++OBJEXT = o ++PACKAGE = phyml ++PACKAGE_BUGREPORT = s.guindon@auckland.ac.nz ++PACKAGE_NAME = PhyML ++PACKAGE_STRING = PhyML 20120412 ++PACKAGE_TARNAME = phyml ++PACKAGE_URL = ++PACKAGE_VERSION = 20120412 ++PATH_SEPARATOR = : ++SET_MAKE = ++SHELL = /bin/sh ++STRIP = ++VERSION = 20120412 ++abs_builddir = /home/guindon/Downloads/phyml-20120412/src ++abs_srcdir = /home/guindon/Downloads/phyml-20120412/src ++abs_top_builddir = /home/guindon/Downloads/phyml-20120412 ++abs_top_srcdir = /home/guindon/Downloads/phyml-20120412 ++ac_ct_CC = gcc ++am__include = include ++am__leading_dot = . ++am__quote = ++am__tar = ${AMTAR} chof - "$$tardir" ++am__untar = ${AMTAR} xf - ++bindir = ${exec_prefix}/bin ++build = x86_64-unknown-linux-gnu ++build_alias = ++build_cpu = x86_64 ++build_os = linux-gnu ++build_vendor = unknown ++builddir = . ++datadir = ${datarootdir} ++datarootdir = ${prefix}/share ++docdir = ${datarootdir}/doc/${PACKAGE_TARNAME} ++dvidir = ${docdir} ++exec_prefix = ${prefix} ++host = x86_64-unknown-linux-gnu ++host_alias = ++host_cpu = x86_64 ++host_os = linux-gnu ++host_vendor = unknown ++htmldir = ${docdir} ++includedir = ${prefix}/include ++infodir = ${datarootdir}/info ++install_sh = ${SHELL} /home/guindon/Downloads/phyml-20120412/install-sh ++libdir = ${exec_prefix}/lib ++libexecdir = ${exec_prefix}/libexec ++localedir = ${datarootdir}/locale ++localstatedir = ${prefix}/var ++mandir = ${datarootdir}/man ++mkdir_p = /usr/bin/mkdir -p ++oldincludedir = /usr/include ++pdfdir = ${docdir} ++prefix = /usr/local ++program_transform_name = s,x,x, ++psdir = ${docdir} ++sbindir = ${exec_prefix}/sbin ++sharedstatedir = ${prefix}/com ++srcdir = . ++sysconfdir = ${prefix}/etc ++target_alias = ++top_build_prefix = ../ ++top_builddir = .. ++top_srcdir = .. ++PROG = PHYML ++#PROG = TEST ++#PROG = PHYML ++#PROG = RF ++#PROG = M4 ++#PROG = TIPORDER ++#PROG = RWRAP ++#PROG = PART ++#PROG = PHYCONT ++#PROG = PHYTIME ++#phytime_SOURCES = main.c \ ++#utilities.c utilities.h\ ++#optimiz.c optimiz.h\ ++#lk.c lk.h\ ++#bionj.c bionj.h\ ++#models.c models.h\ ++#free.c free.h\ ++#help.c help.h\ ++#simu.c simu.h\ ++#eigen.c eigen.h\ ++#pars.c pars.h\ ++#alrt.c alrt.h\ ++#interface.c interface.h\ ++#cl.c cl.h\ ++#spr.c spr.h\ ++#times.c times.h\ ++#m4.c m4.h\ ++#draw.c draw.h\ ++#rates.c rates.h\ ++#mcmc.c mcmc.h\ ++#stats.c stats.h\ ++#mg.c mg.h\ ++#tiporder.c tiporder.h ++ ++#phytime_LDADD = -lm ++#phycont_SOURCES = main.c \ ++#utilities.c utilities.h\ ++#optimiz.c optimiz.h\ ++#lk.c lk.h\ ++#bionj.c bionj.h\ ++#models.c models.h\ ++#free.c free.h\ ++#help.c help.h\ ++#simu.c simu.h\ ++#eigen.c eigen.h\ ++#pars.c pars.h\ ++#alrt.c alrt.h\ ++#interface.c interface.h\ ++#cl.c cl.h\ ++#spr.c spr.h\ ++#times.c times.h\ ++#m4.c m4.h\ ++#draw.c draw.h\ ++#rates.c rates.h\ ++#mcmc.c mcmc.h\ ++#stats.c stats.h\ ++#mg.c mg.h\ ++#tiporder.c tiporder.h ++ ++# continuous.c continuous.h ++#phycont_LDADD = -lm ++# if WANT_RWRAP ++# lib_LTLIBRARIES = librwrap.la ++# librwrap_la_SOURCES = main.c \ ++# utilities.c utilities.h\ ++# optimiz.c optimiz.h\ ++# lk.c lk.h\ ++# bionj.c bionj.h\ ++# models.c models.h\ ++# free.c free.h\ ++# help.c help.h\ ++# simu.c simu.h\ ++# eigen.c eigen.h\ ++# pars.c pars.h\ ++# alrt.c alrt.h\ ++# interface.c interface.h\ ++# cl.c cl.h\ ++# mg.c mg.h\ ++# spr.c spr.h\ ++# m4.c m4.h\ ++# draw.c draw.h\ ++# mcmc.c mcmc.h\ ++# stats.c stats.h\ ++# times.c times.h\ ++# tiporder.c tiporder.h\ ++# rates.c rates.h\ ++# rwrapper.c rwrapper.h ++# librwrap_la_LIBADD = -lm ++# librwrap_la_LDFLAGS = -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -flat_namespace -undefined suppress -shared -module ++# librwrap_la_CFLAGS=-std=gnu99 -fPIC ++# else ++#part_SOURCES = main.c \ ++#utilities.c utilities.h\ ++#optimiz.c optimiz.h\ ++#lk.c lk.h\ ++#bionj.c bionj.h\ ++#models.c models.h\ ++#free.c free.h\ ++#help.c help.h\ ++#simu.c simu.h\ ++#eigen.c eigen.h\ ++#pars.c pars.h\ ++#alrt.c alrt.h\ ++#interface.c interface.h\ ++#cl.c cl.h\ ++#mg.c mg.h\ ++#spr.c spr.h\ ++#m4.c m4.h\ ++#draw.c draw.h\ ++#stats.c stats.h\ ++#tiporder.c tiporder.h ++ ++#part_LDADD = -lm ++#tiporder_SOURCES = main.c \ ++#utilities.c utilities.h\ ++#optimiz.c optimiz.h\ ++#lk.c lk.h\ ++#bionj.c bionj.h\ ++#models.c models.h\ ++#free.c free.h\ ++#help.c help.h\ ++#simu.c simu.h\ ++#eigen.c eigen.h\ ++#pars.c pars.h\ ++#alrt.c alrt.h\ ++#interface.c interface.h\ ++#cl.c cl.h\ ++#mg.c mg.h\ ++#times.c times.h\ ++#mcmc.c mcmc.h\ ++#rates.c rates.h\ ++#spr.c spr.h\ ++#m4.c m4.h\ ++#draw.c draw.h\ ++#stats.c stats.h\ ++#tiporder.c tiporder.h ++ ++#tiporder_LDADD = -lm ++#m4_SOURCES = main.c \ ++#utilities.c utilities.h\ ++#optimiz.c optimiz.h\ ++#lk.c lk.h\ ++#bionj.c bionj.h\ ++#models.c models.h\ ++#free.c free.h\ ++#help.c help.h\ ++#simu.c simu.h\ ++#eigen.c eigen.h\ ++#pars.c pars.h\ ++#alrt.c alrt.h\ ++#interface.c interface.h\ ++#cl.c cl.h\ ++#mg.c mg.h\ ++#times.c times.h\ ++#mcmc.c mcmc.h\ ++#rates.c rates.h\ ++#spr.c spr.h\ ++#draw.c draw.h\ ++#stats.c stats.h\ ++#tiporder.c tiporder.h\ ++#m4.c m4.h ++ ++#m4_LDADD = -lm ++#rf_SOURCES = main.c \ ++#utilities.c utilities.h\ ++#optimiz.c optimiz.h\ ++#lk.c lk.h\ ++#bionj.c bionj.h\ ++#models.c models.h\ ++#free.c free.h\ ++#help.c help.h\ ++#simu.c simu.h\ ++#eigen.c eigen.h\ ++#pars.c pars.h\ ++#alrt.c alrt.h\ ++#interface.c interface.h\ ++#cl.c cl.h\ ++#mg.c mg.h\ ++#times.c times.h\ ++#mcmc.c mcmc.h\ ++#rates.c rates.h\ ++#spr.c spr.h\ ++#draw.c draw.h\ ++#stats.c stats.h\ ++#tiporder.c tiporder.h\ ++#m4.c m4.h ++ ++#rf_LDADD = -lm ++#phyml_mpi_SOURCES = main.c \ ++#utilities.c utilities.h\ ++#optimiz.c optimiz.h\ ++#lk.c lk.h\ ++#bionj.c bionj.h\ ++#models.c models.h\ ++#free.c free.h\ ++#help.c help.h\ ++#simu.c simu.h\ ++#eigen.c eigen.h\ ++#pars.c pars.h\ ++#alrt.c alrt.h\ ++#interface.c interface.h\ ++#cl.c cl.h\ ++#spr.c spr.h\ ++#draw.c draw.h\ ++#mpi_boot.c mpi_boot.h\ ++#stats.c stats.h\ ++#rates.c rates.h\ ++#mcmc.c mcmc.h\ ++#times.c times.h\ ++#tiporder.c tiporder.h\ ++#mg.c mg.h\ ++#m4.c m4.h\ ++#xml.c xml.h ++ ++#phyml_mpi_LDADD = -lm ++#test_SOURCES = main.c \ ++#utilities.c utilities.h\ ++#optimiz.c optimiz.h\ ++#lk.c lk.h\ ++#bionj.c bionj.h\ ++#models.c models.h\ ++#free.c free.h\ ++#help.c help.h\ ++#simu.c simu.h\ ++#eigen.c eigen.h\ ++#pars.c pars.h\ ++#alrt.c alrt.h\ ++#interface.c interface.h\ ++#cl.c cl.h\ ++#spr.c spr.h\ ++#draw.c draw.h\ ++#stats.c stats.h\ ++#rates.c rates.h\ ++#mcmc.c mcmc.h\ ++#times.c times.h\ ++#tiporder.c tiporder.h\ ++#mg.c mg.h\ ++#m4.c m4.h\ ++#xml.c xml.h ++ ++#test_LDADD = -lm ++phyml_SOURCES = main.c \ ++utilities.c utilities.h\ ++optimiz.c optimiz.h\ ++lk.c lk.h\ ++bionj.c bionj.h\ ++models.c models.h\ ++free.c free.h\ ++help.c help.h\ ++simu.c simu.h\ ++eigen.c eigen.h\ ++pars.c pars.h\ ++alrt.c alrt.h\ ++interface.c interface.h\ ++cl.c cl.h\ ++spr.c spr.h\ ++draw.c draw.h\ ++stats.c stats.h\ ++rates.c rates.h\ ++mcmc.c mcmc.h\ ++times.c times.h\ ++tiporder.c tiporder.h\ ++mg.c mg.h\ ++m4.c m4.h ++ ++phyml_LDADD = -lm ++all: all-am ++ ++.SUFFIXES: ++.SUFFIXES: .c .o .obj ++$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps) ++ @for dep in $?; do \ ++ case '$(am__configure_deps)' in \ ++ *$$dep*) \ ++ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \ ++ && { if test -f $@; then exit 0; else break; fi; }; \ ++ exit 1;; \ ++ esac; \ ++ done; \ ++ echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign src/Makefile'; \ ++ $(am__cd) $(top_srcdir) && \ ++ $(AUTOMAKE) --foreign src/Makefile ++.PRECIOUS: Makefile ++Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status ++ @case '$?' in \ ++ *config.status*) \ ++ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \ ++ *) \ ++ echo ' cd $(top_builddir) && $(SHELL) ./config.status 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clean-binPROGRAMS \ ++ clean-generic ctags distclean distclean-compile \ ++ distclean-generic distclean-tags distdir dvi dvi-am html \ ++ html-am info info-am install install-am install-binPROGRAMS \ ++ install-data install-data-am install-dvi install-dvi-am \ ++ install-exec install-exec-am install-html install-html-am \ ++ install-info install-info-am install-man install-pdf \ ++ install-pdf-am install-ps install-ps-am install-strip \ ++ installcheck installcheck-am installdirs maintainer-clean \ ++ maintainer-clean-generic mostlyclean mostlyclean-compile \ ++ mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \ ++ uninstall-am uninstall-binPROGRAMS ++ ++ ++# all-am: intro $(bin_PROGRAMS)$(EXEEXT) ++all-am: intro $(bin_PROGRAMS) ++ @echo "" ++ @echo "Done." ++ ++intro: ++ @echo "" ++ @echo "" ++ @echo ":: Building [$(bin_PROGRAMS)]. Version $(VERSION) ::" ++ @echo "" ++ @echo "" ++ ++# Tell versions [3.59,3.63) of GNU make to not export all variables. ++# Otherwise a system limit (for SysV at least) may be exceeded. ++.NOEXPORT: +unchanged: +--- ./phyml-20120412/src/mcmc.c 2012-03-20 14:10:49.000000000 +1300 ++++ ./phyml-20120412-new-bak/src/mcmc.c 2013-02-18 21:51:51.459662430 +1300 +@@ -1977,7 +1977,7 @@ + if(tree->mod->n_catg > 1) + { + if(tree->mod->free_mixt_rates == NO) +- PhyML_Fprintf(fp,"%G\t",tree->mod->alpha); ++ PhyML_Fprintf(fp,"%G\t",tree->mod->alpha->v); + else + { + For(i,tree->mod->n_catg) PhyML_Fprintf(fp,"%G\t",tree->mod->gamma_r_proba->v[i]); +unchanged: +--- ./phyml-20120412/src/optimiz.c 2012-03-13 19:04:03.000000000 +1300 ++++ ./phyml-20120412-new-bak/src/optimiz.c 2013-02-18 21:51:51.462662427 +1300 +@@ -979,29 +979,18 @@ + + if((tree->mod->s_opt->opt_free_mixt_rates) && (tree->mod->free_mixt_rates == YES)) + { +- /* int failed; */ ++ int failed; + int i; + +- /* failed = 0; */ +- /* tree->mod->update_eigen = 1; */ +- /* BFGS(tree,tree->mod->gamma_r_proba_unscaled,tree->mod->n_catg,1.e-5,1.e-5, */ +- /* &Return_Abs_Lk, */ +- /* &Num_Derivative_Several_Param, */ +- /* &Lnsrch_Free_Mixt_Rates,&failed); */ +- + if(verbose) Print_Lk(tree,"[Rate class freqs. ]"); + ++ failed = 0; ++ tree->mod->update_eigen = 1; ++ BFGS(tree,tree->mod->gamma_r_proba_unscaled,tree->mod->n_catg,1.e-5,1.e-5, ++ &Return_Abs_Lk, ++ &Num_Derivative_Several_Param, ++ &Lnsrch_Free_Mixt_Rates,&failed); + +- /* For(i,tree->mod->n_catg-1) */ +- /* { */ +- /* Generic_Brent_Lk(&(tree->mod->gamma_r_proba_unscaled->v[i]), */ +- /* 0., */ +- /* 100, */ +- /* tree->mod->s_opt->min_diff_lk_global, */ +- /* tree->mod->s_opt->brent_it_max, */ +- /* tree->mod->s_opt->quickdirty, */ +- /* Wrap_Lk,NULL,tree,NULL); */ +- /* } */ + + tree->mod->gamma_r_proba_unscaled->v[tree->mod->n_catg-1] = 100.; + For(i,tree->mod->n_catg-1) +unchanged: +--- ./phyml-20120412/src/tree 1970-01-01 12:00:00.000000000 +1200 ++++ ./phyml-20120412-new-bak/src/tree 2013-02-19 10:09:36.962892889 +1300 +@@ -0,0 +1 @@ ++((((((tax6:0.01,(tax5:0.01,tax1:0.026):0.008):0.003,(tax7:0.003,tax3:0.003):0.01271127):0.01,tax2:0.01):0.01,tax10:0.01):0.01,tax9:0.01):0.01,tax8:0.01,tax4:0.1); +\ No newline at end of file +unchanged: +--- ./phyml-20120412/src/utilities.c 2012-04-11 11:48:30.000000000 +1200 ++++ ./phyml-20120412-new-bak/src/utilities.c 2013-02-19 10:16:57.770281203 +1300 +@@ -1668,6 +1668,7 @@ + + Detect_Align_File_Format(io); + ++ + switch(io->data_file_format) + { + case PHYLIP: +@@ -1861,7 +1862,7 @@ + { + if(!Get_Token(fp,token)) break; + +-/* PhyML_Printf("\n+ Token: '%s' next_token=%d cur_token=%d",token,nxt_token_t,cur_token_t); */ ++ PhyML_Printf("\n+ Token: '%s' next_token=%d cur_token=%d",token,nxt_token_t,cur_token_t); + + if(token[0] == ';') + { +@@ -1940,7 +1941,7 @@ + } + while(c != '"'); + *token = c; +- c = fgetc(fp); ++ /* c = fgetc(fp); */ + if(c == EOF) return 0; + *(token+1) = '\0'; + return 1; +@@ -1950,6 +1951,8 @@ + { + Skip_Comment(fp); + c = fgetc(fp); ++ *token = c; ++ token++; + if(c == EOF) return 0; + return 1; + } +@@ -1967,7 +1970,7 @@ + else if(c == '-') { *token = c; token++; } + else + { +- while(isgraph(c) && c != ';' && c != '-' && c != ',') ++ while(isgraph(c) && c != ';' && c != '-' && c != ',' && c != '=') + { + *(token++) = c; + c = fgetc(fp); +@@ -2308,8 +2311,6 @@ + + } + +- +- + ////////////////////////////////////////////////////////////// + ////////////////////////////////////////////////////////////// + +@@ -7756,7 +7757,7 @@ + + #ifndef PHYTIME + mod->l_min = 1.E-8; +- mod->l_max = 100.0; ++ mod->l_max = 10.0; + #else + mod->l_min = 1.E-8; + mod->l_max = 2.0; +@@ -8049,11 +8050,23 @@ + t_node **bip1, **bip2; + int bip_size1, bip_size2, bip_size; + int different,identical; ++ int n_edges; + + /* !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!*/ + /* WARNING: call Match_Tip_Numbers and Get_Bip before using this function. */ + /* !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!*/ + ++ if(on_existing_edges_only == YES) ++ { ++ n_edges = 0; ++ For(i,2*tree1->n_otu-3) ++ if(tree1->t_edges[i]->does_exist && tree2->t_edges[i]->does_exist) n_edges++; ++ n_edges -= tree1->n_otu; ++ } ++ else ++ { ++ n_edges = tree1->n_otu-3; ++ } + + identical = 0; + different = 0; +@@ -8070,7 +8083,7 @@ + bip_size2 = MIN(b2->left->bip_size[b2->l_r],b2->rght->bip_size[b2->r_l]); + + if(bip_size2 > 1 && ((on_existing_edges_only == YES && b2->does_exist) || (on_existing_edges_only == NO))) +- { ++ { + if(bip_size1 == bip_size2) + { + bip_size = bip_size1; +@@ -8139,17 +8152,21 @@ + b1->bip_score++; + b2->bip_score++; + identical++; +- break; ++ goto out; ++ } ++ else ++ { ++ different++; // Bipartitions have identical sizes but distinct elements + } +- else different++; // Bipartitions has identical size but distinct elements + } + else different++; // Biparition have different sizes + } + } + } ++ out: ; + } +- +- return different; ++ return n_edges - identical; ++ /* return different; */ + } + + ////////////////////////////////////////////////////////////// +@@ -12242,6 +12259,9 @@ + + aLRT(tree); + ++ Br_Len_Involving_Invar(tree); ++ Rescale_Br_Len_Multiplier_Tree(tree); ++ + Free(s_tree); + s_tree = Write_Tree(tree,NO); + +@@ -12481,6 +12501,9 @@ + Warn_And_Exit(""); + } + ++ ++ if(node_list_size == 1) return node_list[0]; ++ + list = (t_node ***)mCalloc(node_list_size,sizeof(t_node **)); + For(i,node_list_size) list[i] = (t_node **)mCalloc(2*tree->n_otu-1,sizeof(t_node *)); + size = (int *)mCalloc(node_list_size,sizeof(int)); +unchanged: +--- ./phyml-20120412/src/utilities.h 2012-04-11 11:39:02.000000000 +1200 ++++ ./phyml-20120412-new-bak/src/utilities.h 2013-02-18 21:51:51.452662435 +1300 +@@ -272,6 +272,8 @@ + /* #define P_LK_LIM_SUP 2.037035976e+90 /\* R: format(2^(+300),digits=10) *\/ */ + #define P_LK_LIM_INF 3.054936e-151 /* 2^-500 */ + #define P_LK_LIM_SUP 3.273391e+150 /* 2^500 */ ++/* #define P_LK_LIM_INF 1.499697e-241 /\* 2^-800 *\/ */ ++/* #define P_LK_LIM_SUP 6.668014e+240 /\* 2^800 *\/ */ + + + /*!********************************************************/ +unchanged: +--- utilities.c 2013-10-31 08:57:09.622430940 +1300 ++++ utilities.new.c 2013-10-31 08:55:49.522433717 +1300 +@@ -4769,8 +4769,6 @@ + t_node *n_e, *n_f; + + n_otu = t_full->n_otu; +- t_empt->n_root = t_full->n_root; +- t_empt->e_root = t_full->e_root; + t_empt->c_lnL_sorted = t_full->c_lnL_sorted; + t_empt->log_site_lk_cat = t_full->log_site_lk_cat; + t_empt->cur_site_lk = t_full->cur_site_lk; +@@ -6993,6 +6991,7 @@ + boot_tree->mat = boot_mat; + } + ++ + boot_tree->mod = boot_mod; + boot_tree->io = tree->io; + boot_tree->data = boot_data; +@@ -7002,6 +7001,7 @@ + boot_tree->io->print_site_lnl = 0; + boot_tree->io->print_trace = 0; + ++ + if((boot_tree->mod->s_opt->random_input_tree) && (boot_tree->mod->s_opt->topo_search == SPR_MOVE)) Random_Tree(boot_tree); + Order_Tree_CSeq(boot_tree,boot_data); + Share_Lk_Struct(tree,boot_tree); +@@ -7010,6 +7010,7 @@ + Fill_Dir_Table(boot_tree); + Update_Dirs(boot_tree); + ++ + if(tree->mod->s_opt->greedy) Init_P_Lk_Tips_Double(boot_tree); + else Init_P_Lk_Tips_Int(boot_tree); + Init_Ui_Tips(boot_tree); +@@ -13307,11 +13308,15 @@ + Warn_And_Exit(""); + } + ++ has_outgrp = NO; ++ ++ /* 'Root' node is t_nodes[0] */ + if(strstr(tree->t_nodes[0]->name,"*")) + { + /* PhyML_Printf("\n. Found outgroup taxon: %s",tree->t_nodes[0]->name); */ + tree->t_nodes[0]->s_ingrp[0] = 0; + tree->t_nodes[0]->s_outgrp[0] = 1; ++ has_outgrp = YES; + } + else + { +@@ -13319,7 +13324,6 @@ + tree->t_nodes[0]->s_outgrp[0] = 0; + } + +- has_outgrp = NO; + Get_Best_Root_Position_Post(tree->t_nodes[0],tree->t_nodes[0]->v[0],&has_outgrp,tree); + Get_Best_Root_Position_Pre(tree->t_nodes[0],tree->t_nodes[0]->v[0],tree); + +only in patch2: +unchanged: +--- src/utilities.c 2012-04-11 11:48:30.000000000 +1200 ++++ src.new/utilities.c 2013-11-12 14:19:11.600689913 +1300 +@@ -13995,7 +13995,7 @@ int Check_Topo_Constraints(t_tree *big_t + For(i,2*big_tree_cpy->n_otu-3) big_tree_cpy->t_edges[i]->bip_score = 0; + For(i,2*small_tree->n_otu-3) small_tree->t_edges[i]->bip_score = 0; + +- diffs = Compare_Bip(small_tree,big_tree_cpy,YES); ++ diffs = Compare_Bip(small_tree,big_tree_cpy,NO); + + /* printf("\n"); */ + /* printf("\n. %s",Write_Tree(big_tree_cpy,NO)); */ |