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-rw-r--r--academic/PhyML/20131112.patch1591
-rw-r--r--academic/PhyML/PhyML.SlackBuild61
-rw-r--r--academic/PhyML/PhyML.info10
-rw-r--r--academic/PhyML/README10
-rw-r--r--academic/PhyML/slack-desc2
5 files changed, 62 insertions, 1612 deletions
diff --git a/academic/PhyML/20131112.patch b/academic/PhyML/20131112.patch
deleted file mode 100644
index e7eb2670b6..0000000000
--- a/academic/PhyML/20131112.patch
+++ /dev/null
@@ -1,1591 +0,0 @@
-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)
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-+test_DEPENDENCIES =
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-+ 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
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-+# 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)
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-+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
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-+ *config.status*) \
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-+part$(EXEEXT): $(part_OBJECTS) $(part_DEPENDENCIES)
-+ @rm -f part$(EXEEXT)
-+ $(AM_V_CCLD)$(LINK) $(part_OBJECTS) $(part_LDADD) $(LIBS)
-+phycont$(EXEEXT): $(phycont_OBJECTS) $(phycont_DEPENDENCIES)
-+ @rm -f phycont$(EXEEXT)
-+ $(AM_V_CCLD)$(LINK) $(phycont_OBJECTS) $(phycont_LDADD) $(LIBS)
-+phyml$(EXEEXT): $(phyml_OBJECTS) $(phyml_DEPENDENCIES)
-+ @rm -f phyml$(EXEEXT)
-+ $(AM_V_CCLD)$(LINK) $(phyml_OBJECTS) $(phyml_LDADD) $(LIBS)
-+phyml-mpi$(EXEEXT): $(phyml_mpi_OBJECTS) $(phyml_mpi_DEPENDENCIES)
-+ @rm -f phyml-mpi$(EXEEXT)
-+ $(AM_V_CCLD)$(LINK) $(phyml_mpi_OBJECTS) $(phyml_mpi_LDADD) $(LIBS)
-+phytime$(EXEEXT): $(phytime_OBJECTS) $(phytime_DEPENDENCIES)
-+ @rm -f phytime$(EXEEXT)
-+ $(AM_V_CCLD)$(LINK) $(phytime_OBJECTS) $(phytime_LDADD) $(LIBS)
-+rf$(EXEEXT): $(rf_OBJECTS) $(rf_DEPENDENCIES)
-+ @rm -f rf$(EXEEXT)
-+ $(AM_V_CCLD)$(LINK) $(rf_OBJECTS) $(rf_LDADD) $(LIBS)
-+test$(EXEEXT): $(test_OBJECTS) $(test_DEPENDENCIES)
-+ @rm -f test$(EXEEXT)
-+ $(AM_V_CCLD)$(LINK) $(test_OBJECTS) $(test_LDADD) $(LIBS)
-+tiporder$(EXEEXT): $(tiporder_OBJECTS) $(tiporder_DEPENDENCIES)
-+ @rm -f tiporder$(EXEEXT)
-+ $(AM_V_CCLD)$(LINK) $(tiporder_OBJECTS) $(tiporder_LDADD) $(LIBS)
-+
-+mostlyclean-compile:
-+ -rm -f *.$(OBJEXT)
-+
-+distclean-compile:
-+ -rm -f *.tab.c
-+
-+include ./$(DEPDIR)/alrt.Po
-+include ./$(DEPDIR)/bionj.Po
-+include ./$(DEPDIR)/cl.Po
-+include ./$(DEPDIR)/draw.Po
-+include ./$(DEPDIR)/eigen.Po
-+include ./$(DEPDIR)/free.Po
-+include ./$(DEPDIR)/help.Po
-+include ./$(DEPDIR)/interface.Po
-+include ./$(DEPDIR)/lk.Po
-+include ./$(DEPDIR)/m4.Po
-+include ./$(DEPDIR)/main.Po
-+include ./$(DEPDIR)/mcmc.Po
-+include ./$(DEPDIR)/mg.Po
-+include ./$(DEPDIR)/models.Po
-+include ./$(DEPDIR)/mpi_boot.Po
-+include ./$(DEPDIR)/optimiz.Po
-+include ./$(DEPDIR)/pars.Po
-+include ./$(DEPDIR)/rates.Po
-+include ./$(DEPDIR)/simu.Po
-+include ./$(DEPDIR)/spr.Po
-+include ./$(DEPDIR)/stats.Po
-+include ./$(DEPDIR)/times.Po
-+include ./$(DEPDIR)/tiporder.Po
-+include ./$(DEPDIR)/utilities.Po
-+include ./$(DEPDIR)/xml.Po
-+
-+.c.o:
-+ $(AM_V_CC)$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
-+ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+# $(AM_V_CC) \
-+# source='$<' object='$@' libtool=no \
-+# DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) \
-+# $(COMPILE) -c $<
-+
-+.c.obj:
-+ $(AM_V_CC)$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
-+ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
-+# $(AM_V_CC) \
-+# source='$<' object='$@' libtool=no \
-+# DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) \
-+# $(COMPILE) -c `$(CYGPATH_W) '$<'`
-+
-+ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ mkid -fID $$unique
-+tags: TAGS
-+
-+TAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ set x; \
-+ here=`pwd`; \
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ shift; \
-+ if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
-+ test -n "$$unique" || unique=$$empty_fix; \
-+ if test $$# -gt 0; then \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ "$$@" $$unique; \
-+ else \
-+ $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
-+ $$unique; \
-+ fi; \
-+ fi
-+ctags: CTAGS
-+CTAGS: $(HEADERS) $(SOURCES) $(TAGS_DEPENDENCIES) \
-+ $(TAGS_FILES) $(LISP)
-+ list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
-+ unique=`for i in $$list; do \
-+ if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
-+ done | \
-+ $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
-+ END { if (nonempty) { for (i in files) print i; }; }'`; \
-+ test -z "$(CTAGS_ARGS)$$unique" \
-+ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
-+ $$unique
-+
-+GTAGS:
-+ here=`$(am__cd) $(top_builddir) && pwd` \
-+ && $(am__cd) $(top_srcdir) \
-+ && gtags -i $(GTAGS_ARGS) "$$here"
-+
-+distclean-tags:
-+ -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
-+
-+distdir: $(DISTFILES)
-+ @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
-+ list='$(DISTFILES)'; \
-+ dist_files=`for file in $$list; do echo $$file; done | \
-+ sed -e "s|^$$srcdirstrip/||;t" \
-+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
-+ case $$dist_files in \
-+ */*) $(MKDIR_P) `echo "$$dist_files" | \
-+ sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
-+ sort -u` ;; \
-+ esac; \
-+ for file in $$dist_files; do \
-+ if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
-+ if test -d $$d/$$file; then \
-+ dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
-+ if test -d "$(distdir)/$$file"; then \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
-+ cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
-+ find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
-+ fi; \
-+ cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
-+ else \
-+ test -f "$(distdir)/$$file" \
-+ || cp -p $$d/$$file "$(distdir)/$$file" \
-+ || exit 1; \
-+ fi; \
-+ done
-+check-am: all-am
-+check: check-am
-+all-am: Makefile $(PROGRAMS)
-+installdirs:
-+ for dir in "$(DESTDIR)$(bindir)"; do \
-+ test -z "$$dir" || $(MKDIR_P) "$$dir"; \
-+ done
-+install: install-am
-+install-exec: install-exec-am
-+install-data: install-data-am
-+uninstall: uninstall-am
-+
-+install-am: all-am
-+ @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
-+
-+installcheck: installcheck-am
-+install-strip:
-+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
-+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
-+ `test -z '$(STRIP)' || \
-+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
-+mostlyclean-generic:
-+
-+clean-generic:
-+
-+distclean-generic:
-+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-+ -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
-+
-+maintainer-clean-generic:
-+ @echo "This command is intended for maintainers to use"
-+ @echo "it deletes files that may require special tools to rebuild."
-+clean: clean-am
-+
-+clean-am: clean-binPROGRAMS clean-generic mostlyclean-am
-+
-+distclean: distclean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+distclean-am: clean-am distclean-compile distclean-generic \
-+ distclean-tags
-+
-+dvi: dvi-am
-+
-+dvi-am:
-+
-+html: html-am
-+
-+html-am:
-+
-+info: info-am
-+
-+info-am:
-+
-+install-data-am:
-+
-+install-dvi: install-dvi-am
-+
-+install-dvi-am:
-+
-+install-exec-am: install-binPROGRAMS
-+
-+install-html: install-html-am
-+
-+install-html-am:
-+
-+install-info: install-info-am
-+
-+install-info-am:
-+
-+install-man:
-+
-+install-pdf: install-pdf-am
-+
-+install-pdf-am:
-+
-+install-ps: install-ps-am
-+
-+install-ps-am:
-+
-+installcheck-am:
-+
-+maintainer-clean: maintainer-clean-am
-+ -rm -rf ./$(DEPDIR)
-+ -rm -f Makefile
-+maintainer-clean-am: distclean-am maintainer-clean-generic
-+
-+mostlyclean: mostlyclean-am
-+
-+mostlyclean-am: mostlyclean-compile mostlyclean-generic
-+
-+pdf: pdf-am
-+
-+pdf-am:
-+
-+ps: ps-am
-+
-+ps-am:
-+
-+uninstall-am: uninstall-binPROGRAMS
-+
-+.MAKE: install-am install-strip
-+
-+.PHONY: CTAGS GTAGS all all-am check check-am clean 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)); */
diff --git a/academic/PhyML/PhyML.SlackBuild b/academic/PhyML/PhyML.SlackBuild
index 6c8ccdd3a4..d4b3d67cae 100644
--- a/academic/PhyML/PhyML.SlackBuild
+++ b/academic/PhyML/PhyML.SlackBuild
@@ -25,16 +25,16 @@
# Thanks to Niels Horn for some handy modifications and corrections.
PRGNAM=PhyML
-VERSION=${VERSION:-20131112}
+VERSION=${VERSION:-3.2.20160530}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
SRCNAM=$(echo $PRGNAM | tr A-Z a-z)
-SRCVER=20120412
+SRCVER=3.2.20160530
if [ -z "$ARCH" ]; then
case "$( uname -m )" in
- i?86) ARCH=i486 ;;
+ i?86) ARCH=i586 ;;
arm*) ARCH=arm ;;
*) ARCH=$( uname -m ) ;;
esac
@@ -45,8 +45,8 @@ TMP=${TMP:-/tmp/SBo}
PKG=$TMP/package-$PRGNAM
OUTPUT=${OUTPUT:-/tmp}
-if [ "$ARCH" = "i486" ]; then
- SLKCFLAGS="-O2 -march=i486 -mtune=i686"
+if [ "$ARCH" = "i586" ]; then
+ SLKCFLAGS="-O2 -march=i586 -mtune=i686"
LIBDIRSUFFIX=""
elif [ "$ARCH" = "i686" ]; then
SLKCFLAGS="-O2 -march=i686 -mtune=i686"
@@ -65,7 +65,13 @@ rm -rf $PKG
mkdir -p $TMP $PKG $OUTPUT
cd $TMP
rm -rf $SRCNAM-$SRCVER
-tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz
+
+if [ -e $CWD/v${SRCVER}.tar.gz ]; then
+ tar xvf $CWD/v${SRCVER}.tar.gz
+else
+ tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz
+fi
+
cd $SRCNAM-$SRCVER
chown -R root:root .
find -L . \
@@ -74,18 +80,38 @@ find -L . \
\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
-# Apply version patch
-cd src
- patch -i $CWD/$VERSION.patch
-cd ..
+# This is PhyML, the main component of the package. If this is all you want, you
+# can comment out the sections that build PhyML MPI and Phyrex below.
+./autogen.sh
+./configure \
+ --prefix=/usr \
+ --libdir=/usr/lib${LIBDIRSUFFIX} \
+ --sysconfdir=/etc \
+ --localstatedir=/var \
+ --mandir=/usr/man \
+ --enable-phyml \
+ --docdir=/usr/doc/$PRGNAM-$VERSION \
+ --build=$ARCH-slackware-linux
-# This is PhyML
+# Use our CFLAGS
+sed -i "/^CFLAGS/s/=/+=/" src/Makefile
+sed -i "/^CFLAGS/s/=/+=/" Makefile
+
+CFLAGS="$SLKCFLAGS" \
+CXXFLAGS="$SLKCFLAGS" \
+make
+make install DESTDIR=$PKG
+
+# This is PhyML MPI. If you do not want it, comment the lines below. Then you do
+# not need to install openmpi.
+./autogen.sh
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
+ --enable-mpi \
--docdir=/usr/doc/$PRGNAM-$VERSION \
--build=$ARCH-slackware-linux
@@ -98,14 +124,15 @@ CXXFLAGS="$SLKCFLAGS" \
make
make install DESTDIR=$PKG
-# And this is PhyTime
+# This is Phyrex
+./autogen.sh
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
- --enable-phytime \
--mandir=/usr/man \
+ --enable-phyrex \
--docdir=/usr/doc/$PRGNAM-$VERSION \
--build=$ARCH-slackware-linux
@@ -121,9 +148,15 @@ make install DESTDIR=$PKG
find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
| cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
+# Include some examples
+mkdir -p $PKG/usr/share/$PRGNAM
+cp -a \
+ examples/{lg4x,phyrex_input_files,nexus_example.nxs,nucleic,proteic} \
+ $PKG/usr/share/$PRGNAM
+
mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
cp -a \
- doc/$SRCNAM-manual-20120306.pdf AUTHORS ChangeLog COPYING INSTALL README \
+ doc/$SRCNAM-manual.pdf AUTHORS ChangeLog COPYING LICENSE README \
$PKG/usr/doc/$PRGNAM-$VERSION
cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
diff --git a/academic/PhyML/PhyML.info b/academic/PhyML/PhyML.info
index dd1f897135..739d1befc0 100644
--- a/academic/PhyML/PhyML.info
+++ b/academic/PhyML/PhyML.info
@@ -1,10 +1,10 @@
PRGNAM="PhyML"
-VERSION="20131112"
-HOMEPAGE="http://code.google.com/p/phyml/"
-DOWNLOAD="http://phyml.googlecode.com/files/phyml-20120412.tar.gz"
-MD5SUM="d2207a3d6caf633c43239a01ce70f244"
+VERSION="3.2.20160530"
+HOMEPAGE="https://github.com/stephaneguindon/phyml/"
+DOWNLOAD="https://github.com/stephaneguindon/phyml/archive/v3.2.20160530.tar.gz"
+MD5SUM="7a4689e2de3ac9efd7586980b07331f0"
DOWNLOAD_x86_64=""
MD5SUM_x86_64=""
-REQUIRES=""
+REQUIRES="openmpi"
MAINTAINER="Petar Petrov"
EMAIL="slackalaxy@gmail.com"
diff --git a/academic/PhyML/README b/academic/PhyML/README
index 60178833a8..fd66cda123 100644
--- a/academic/PhyML/README
+++ b/academic/PhyML/README
@@ -9,7 +9,15 @@ It also implements two methods to evaluate branch supports in a sound
statistical framework (the non-parametric bootstrap and the
approximate likelihood ratio test).
-The script also builds the additional program PhyTime.
+NOTE 1: This also builds Phyrex and the MPI (using multiple processors)
+version of PhyML. The executable of the latter is called phyml-mpi and
+requires openmpi. If you do not want them to be built in the package,
+check the SlackBuild script.
+
+NOTE 2: PhyTime used to be part of the PhyML package. However, PhyTime
+from the latest releases of PhyML does not build anymore. meanwhile,
+PhyTime is available separately, which installs the latest version that
+builds.
For details and citation
New Algorithms and Methods to Estimate Maximum-Likelihood
diff --git a/academic/PhyML/slack-desc b/academic/PhyML/slack-desc
index 76f3459318..ae498120bb 100644
--- a/academic/PhyML/slack-desc
+++ b/academic/PhyML/slack-desc
@@ -14,6 +14,6 @@ PhyML: wide range of options that were designed to facilitate standard
PhyML: phylogenetic analyses.
PhyML:
PhyML: Home: http://code.google.com/p/phyml/
-PhyML: References: /usr/doc/PhyML-20131112/References
+PhyML: References: /usr/doc/PhyML-3.2.20160530/References
PhyML:
PhyML: