academic/PhyML: Updated for version 3.2.20160530.

Signed-off-by: David Spencer <idlemoor@slackbuilds.org>

5 files changed, 62 insertions, 1612 deletions

diff --git a/academic/PhyML/20131112.patch b/academic/PhyML/20131112.patch
deleted file mode 100644
index e7eb2670b6f5..000000000000
--- 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 =
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-+	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
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-+#	optimiz.$(OBJEXT) \
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-+#	bionj.$(OBJEXT) \
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-+#	mg.$(OBJEXT) \
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-+#	mcmc.$(OBJEXT) \
-+#	rates.$(OBJEXT) \
-+#	spr.$(OBJEXT) \
-+#	draw.$(OBJEXT) \
-+#	stats.$(OBJEXT) \
-+#	tiporder.$(OBJEXT) \
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-+	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
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-+#	utilities.$(OBJEXT) \
-+#	optimiz.$(OBJEXT) \
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-+#	bionj.$(OBJEXT) \
-+#	models.$(OBJEXT) \
-+#	free.$(OBJEXT) \
-+#	help.$(OBJEXT) \
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-+#	alrt.$(OBJEXT) \
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-+#	spr.$(OBJEXT) \
-+#	draw.$(OBJEXT) \
-+#	stats.$(OBJEXT) \
-+#	rates.$(OBJEXT) \
-+#	mcmc.$(OBJEXT) \
-+#	times.$(OBJEXT) \
-+#	tiporder.$(OBJEXT) \
-+#	mg.$(OBJEXT) \
-+#	m4.$(OBJEXT) \
-+#	xml.$(OBJEXT)
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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
-+#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)
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-+am__mv = mv -f
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-+am__v_GEN_0 = @echo "  GEN   " $@;
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-+PACKAGE_STRING = PhyML 20120412
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-+abs_srcdir = /home/guindon/Downloads/phyml-20120412/src
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-+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 
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-+
-+.SUFFIXES:
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-+	    *$$dep*) \
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-+	        && { if test -f $@; then exit 0; else break; fi; }; \
-+	      exit 1;; \
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-+	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 $(subdir)/$@ $(am__depfiles_maybe)'; \
-+	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
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-+	test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
-+	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
-+	for p in $$list; do echo "$$p $$p"; done | \
-+	sed 's/$(EXEEXT)$$//' | \
-+	while read p p1; do if test -f $$p; \
-+	  then echo "$$p"; echo "$$p"; else :; fi; \
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-+	    -e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
-+	sed 'N;N;N;s,\n, ,g' | \
-+	$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
-+	  { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
-+	    if ($$2 == $$4) files[d] = files[d] " " $$1; \
-+	    else { print "f", $$3 "/" $$4, $$1; } } \
-+	  END { for (d in files) print "f", d, files[d] }' | \
-+	while read type dir files; do \
-+	    if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
-+	    test -z "$$files" || { \
-+	      echo " $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \
-+	      $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
-+	    } \
-+	; done
-+
-+uninstall-binPROGRAMS:
-+	@$(NORMAL_UNINSTALL)
-+	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
-+	files=`for p in $$list; do echo "$$p"; done | \
-+	  sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
-+	      -e 's/$$/$(EXEEXT)/' `; \
-+	test -n "$$list" || exit 0; \
-+	echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
-+	cd "$(DESTDIR)$(bindir)" && rm -f $$files
-+
-+clean-binPROGRAMS:
-+	-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
-+m4$(EXEEXT): $(m4_OBJECTS) $(m4_DEPENDENCIES) 
-+	@rm -f m4$(EXEEXT)
-+	$(AM_V_CCLD)$(LINK) $(m4_OBJECTS) $(m4_LDADD) $(LIBS)
-+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 6c8ccdd3a414..d4b3d67cae7a 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 dd1f897135bd..739d1befc05e 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 60178833a84c..fd66cda1231a 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 76f34593184a..ae498120bb24 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: