Common subdirectories: ./phyml-20120412/src/.deps and ./phyml-20120412-new-bak/src/.deps
diff -uN ./phyml-20120412/src/help.c ./phyml-20120412-new-bak/src/help.c
--- ./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");
 
diff -uN ./phyml-20120412/src/lk.c ./phyml-20120412-new-bak/src/lk.c
--- ./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] ;
 		}
diff -uN ./phyml-20120412/src/Makefile ./phyml-20120412-new-bak/src/Makefile
--- ./phyml-20120412/src/Makefile	1970-01-01 12:00:00.000000000 +1200
+++ ./phyml-20120412-new-bak/src/Makefile	2013-02-18 21:54:46.957806553 +1300
@@ -0,0 +1,1082 @@
+# Makefile.in generated by automake 1.11.1 from Makefile.am.
+# src/Makefile.  Generated from Makefile.in by configure.
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009  Free Software Foundation,
+# Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+
+
+
+pkgdatadir = $(datadir)/phyml
+pkgincludedir = $(includedir)/phyml
+pkglibdir = $(libdir)/phyml
+pkglibexecdir = $(libexecdir)/phyml
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = x86_64-unknown-linux-gnu
+host_triplet = x86_64-unknown-linux-gnu
+bin_PROGRAMS = phyml$(EXEEXT)
+#bin_PROGRAMS = test$(EXEEXT)
+#bin_PROGRAMS = phyml-mpi$(EXEEXT)
+#bin_PROGRAMS = rf$(EXEEXT)
+#bin_PROGRAMS = m4$(EXEEXT)
+#bin_PROGRAMS = tiporder$(EXEEXT)
+#bin_PROGRAMS = part$(EXEEXT)
+#bin_PROGRAMS =  \
+#	phycont$(EXEEXT)
+#bin_PROGRAMS = phytime$(EXEEXT)
+subdir = src
+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+	$(ACLOCAL_M4)
+mkinstalldirs = $(install_sh) -d
+CONFIG_HEADER = $(top_builddir)/config.h
+CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_VPATH_FILES =
+am__installdirs = "$(DESTDIR)$(bindir)"
+PROGRAMS = $(bin_PROGRAMS)
+am__m4_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \
+	optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \
+	free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \
+	pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h mg.c \
+	mg.h times.c times.h mcmc.c mcmc.h rates.c rates.h spr.c spr.h \
+	draw.c draw.h stats.c stats.h tiporder.c tiporder.h m4.c m4.h
+#am_m4_OBJECTS = main.$(OBJEXT) \
+#	utilities.$(OBJEXT) \
+#	optimiz.$(OBJEXT) \
+#	lk.$(OBJEXT) \
+#	bionj.$(OBJEXT) \
+#	models.$(OBJEXT) \
+#	free.$(OBJEXT) \
+#	help.$(OBJEXT) \
+#	simu.$(OBJEXT) \
+#	eigen.$(OBJEXT) \
+#	pars.$(OBJEXT) \
+#	alrt.$(OBJEXT) \
+#	interface.$(OBJEXT) \
+#	cl.$(OBJEXT) \
+#	mg.$(OBJEXT) \
+#	times.$(OBJEXT) \
+#	mcmc.$(OBJEXT) \
+#	rates.$(OBJEXT) \
+#	spr.$(OBJEXT) \
+#	draw.$(OBJEXT) \
+#	stats.$(OBJEXT) \
+#	tiporder.$(OBJEXT) \
+#	m4.$(OBJEXT)
+m4_OBJECTS = $(am_m4_OBJECTS)
+m4_DEPENDENCIES =
+am__part_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \
+	optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \
+	free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \
+	pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h mg.c \
+	mg.h spr.c spr.h m4.c m4.h draw.c draw.h stats.c stats.h \
+	tiporder.c tiporder.h
+#am_part_OBJECTS = main.$(OBJEXT) \
+#	utilities.$(OBJEXT) \
+#	optimiz.$(OBJEXT) \
+#	lk.$(OBJEXT) \
+#	bionj.$(OBJEXT) \
+#	models.$(OBJEXT) \
+#	free.$(OBJEXT) \
+#	help.$(OBJEXT) \
+#	simu.$(OBJEXT) \
+#	eigen.$(OBJEXT) \
+#	pars.$(OBJEXT) \
+#	alrt.$(OBJEXT) \
+#	interface.$(OBJEXT) \
+#	cl.$(OBJEXT) \
+#	mg.$(OBJEXT) \
+#	spr.$(OBJEXT) \
+#	m4.$(OBJEXT) \
+#	draw.$(OBJEXT) \
+#	stats.$(OBJEXT) \
+#	tiporder.$(OBJEXT)
+part_OBJECTS = $(am_part_OBJECTS)
+part_DEPENDENCIES =
+am__phycont_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \
+	optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \
+	free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \
+	pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h spr.c \
+	spr.h times.c times.h m4.c m4.h draw.c draw.h rates.c rates.h \
+	mcmc.c mcmc.h stats.c stats.h mg.c mg.h tiporder.c tiporder.h
+#am_phycont_OBJECTS =  \
+#	main.$(OBJEXT) \
+#	utilities.$(OBJEXT) \
+#	optimiz.$(OBJEXT) \
+#	lk.$(OBJEXT) \
+#	bionj.$(OBJEXT) \
+#	models.$(OBJEXT) \
+#	free.$(OBJEXT) \
+#	help.$(OBJEXT) \
+#	simu.$(OBJEXT) \
+#	eigen.$(OBJEXT) \
+#	pars.$(OBJEXT) \
+#	alrt.$(OBJEXT) \
+#	interface.$(OBJEXT) \
+#	cl.$(OBJEXT) \
+#	spr.$(OBJEXT) \
+#	times.$(OBJEXT) \
+#	m4.$(OBJEXT) \
+#	draw.$(OBJEXT) \
+#	rates.$(OBJEXT) \
+#	mcmc.$(OBJEXT) \
+#	stats.$(OBJEXT) \
+#	mg.$(OBJEXT) \
+#	tiporder.$(OBJEXT)
+phycont_OBJECTS = $(am_phycont_OBJECTS)
+phycont_DEPENDENCIES =
+am__phyml_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \
+	optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \
+	free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \
+	pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h spr.c \
+	spr.h draw.c draw.h stats.c stats.h rates.c rates.h mcmc.c \
+	mcmc.h times.c times.h tiporder.c tiporder.h mg.c mg.h m4.c \
+	m4.h
+am_phyml_OBJECTS = main.$(OBJEXT) \
+	utilities.$(OBJEXT) \
+	optimiz.$(OBJEXT) \
+	lk.$(OBJEXT) \
+	bionj.$(OBJEXT) \
+	models.$(OBJEXT) \
+	free.$(OBJEXT) \
+	help.$(OBJEXT) \
+	simu.$(OBJEXT) \
+	eigen.$(OBJEXT) \
+	pars.$(OBJEXT) \
+	alrt.$(OBJEXT) \
+	interface.$(OBJEXT) \
+	cl.$(OBJEXT) \
+	spr.$(OBJEXT) \
+	draw.$(OBJEXT) \
+	stats.$(OBJEXT) \
+	rates.$(OBJEXT) \
+	mcmc.$(OBJEXT) \
+	times.$(OBJEXT) \
+	tiporder.$(OBJEXT) \
+	mg.$(OBJEXT) \
+	m4.$(OBJEXT)
+phyml_OBJECTS = $(am_phyml_OBJECTS)
+phyml_DEPENDENCIES =
+am__phyml_mpi_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \
+	optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \
+	free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \
+	pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h spr.c \
+	spr.h draw.c draw.h mpi_boot.c mpi_boot.h stats.c stats.h \
+	rates.c rates.h mcmc.c mcmc.h times.c times.h tiporder.c \
+	tiporder.h mg.c mg.h m4.c m4.h xml.c xml.h
+#am_phyml_mpi_OBJECTS = main.$(OBJEXT) \
+#	utilities.$(OBJEXT) \
+#	optimiz.$(OBJEXT) \
+#	lk.$(OBJEXT) \
+#	bionj.$(OBJEXT) \
+#	models.$(OBJEXT) \
+#	free.$(OBJEXT) \
+#	help.$(OBJEXT) \
+#	simu.$(OBJEXT) \
+#	eigen.$(OBJEXT) \
+#	pars.$(OBJEXT) \
+#	alrt.$(OBJEXT) \
+#	interface.$(OBJEXT) \
+#	cl.$(OBJEXT) \
+#	spr.$(OBJEXT) \
+#	draw.$(OBJEXT) \
+#	mpi_boot.$(OBJEXT) \
+#	stats.$(OBJEXT) \
+#	rates.$(OBJEXT) \
+#	mcmc.$(OBJEXT) \
+#	times.$(OBJEXT) \
+#	tiporder.$(OBJEXT) \
+#	mg.$(OBJEXT) \
+#	m4.$(OBJEXT) \
+#	xml.$(OBJEXT)
+phyml_mpi_OBJECTS = $(am_phyml_mpi_OBJECTS)
+phyml_mpi_DEPENDENCIES =
+am__phytime_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \
+	optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \
+	free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \
+	pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h spr.c \
+	spr.h times.c times.h m4.c m4.h draw.c draw.h rates.c rates.h \
+	mcmc.c mcmc.h stats.c stats.h mg.c mg.h tiporder.c tiporder.h
+#am_phytime_OBJECTS = main.$(OBJEXT) \
+#	utilities.$(OBJEXT) optimiz.$(OBJEXT) \
+#	lk.$(OBJEXT) bionj.$(OBJEXT) \
+#	models.$(OBJEXT) free.$(OBJEXT) \
+#	help.$(OBJEXT) simu.$(OBJEXT) \
+#	eigen.$(OBJEXT) pars.$(OBJEXT) \
+#	alrt.$(OBJEXT) interface.$(OBJEXT) \
+#	cl.$(OBJEXT) spr.$(OBJEXT) times.$(OBJEXT) \
+#	m4.$(OBJEXT) draw.$(OBJEXT) rates.$(OBJEXT) \
+#	mcmc.$(OBJEXT) stats.$(OBJEXT) mg.$(OBJEXT) \
+#	tiporder.$(OBJEXT)
+phytime_OBJECTS = $(am_phytime_OBJECTS)
+phytime_DEPENDENCIES =
+am__rf_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \
+	optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \
+	free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \
+	pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h mg.c \
+	mg.h times.c times.h mcmc.c mcmc.h rates.c rates.h spr.c spr.h \
+	draw.c draw.h stats.c stats.h tiporder.c tiporder.h m4.c m4.h
+#am_rf_OBJECTS = main.$(OBJEXT) \
+#	utilities.$(OBJEXT) \
+#	optimiz.$(OBJEXT) \
+#	lk.$(OBJEXT) \
+#	bionj.$(OBJEXT) \
+#	models.$(OBJEXT) \
+#	free.$(OBJEXT) \
+#	help.$(OBJEXT) \
+#	simu.$(OBJEXT) \
+#	eigen.$(OBJEXT) \
+#	pars.$(OBJEXT) \
+#	alrt.$(OBJEXT) \
+#	interface.$(OBJEXT) \
+#	cl.$(OBJEXT) \
+#	mg.$(OBJEXT) \
+#	times.$(OBJEXT) \
+#	mcmc.$(OBJEXT) \
+#	rates.$(OBJEXT) \
+#	spr.$(OBJEXT) \
+#	draw.$(OBJEXT) \
+#	stats.$(OBJEXT) \
+#	tiporder.$(OBJEXT) \
+#	m4.$(OBJEXT)
+rf_OBJECTS = $(am_rf_OBJECTS)
+rf_DEPENDENCIES =
+am__test_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \
+	optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \
+	free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \
+	pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h spr.c \
+	spr.h draw.c draw.h stats.c stats.h rates.c rates.h mcmc.c \
+	mcmc.h times.c times.h tiporder.c tiporder.h mg.c mg.h m4.c \
+	m4.h xml.c xml.h
+#am_test_OBJECTS = main.$(OBJEXT) \
+#	utilities.$(OBJEXT) \
+#	optimiz.$(OBJEXT) \
+#	lk.$(OBJEXT) \
+#	bionj.$(OBJEXT) \
+#	models.$(OBJEXT) \
+#	free.$(OBJEXT) \
+#	help.$(OBJEXT) \
+#	simu.$(OBJEXT) \
+#	eigen.$(OBJEXT) \
+#	pars.$(OBJEXT) \
+#	alrt.$(OBJEXT) \
+#	interface.$(OBJEXT) \
+#	cl.$(OBJEXT) \
+#	spr.$(OBJEXT) \
+#	draw.$(OBJEXT) \
+#	stats.$(OBJEXT) \
+#	rates.$(OBJEXT) \
+#	mcmc.$(OBJEXT) \
+#	times.$(OBJEXT) \
+#	tiporder.$(OBJEXT) \
+#	mg.$(OBJEXT) \
+#	m4.$(OBJEXT) \
+#	xml.$(OBJEXT)
+test_OBJECTS = $(am_test_OBJECTS)
+test_DEPENDENCIES =
+am__tiporder_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \
+	optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \
+	free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \
+	pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h mg.c \
+	mg.h times.c times.h mcmc.c mcmc.h rates.c rates.h spr.c spr.h \
+	m4.c m4.h draw.c draw.h stats.c stats.h tiporder.c tiporder.h
+#am_tiporder_OBJECTS = main.$(OBJEXT) \
+#	utilities.$(OBJEXT) \
+#	optimiz.$(OBJEXT) \
+#	lk.$(OBJEXT) \
+#	bionj.$(OBJEXT) \
+#	models.$(OBJEXT) \
+#	free.$(OBJEXT) \
+#	help.$(OBJEXT) \
+#	simu.$(OBJEXT) \
+#	eigen.$(OBJEXT) \
+#	pars.$(OBJEXT) \
+#	alrt.$(OBJEXT) \
+#	interface.$(OBJEXT) \
+#	cl.$(OBJEXT) \
+#	mg.$(OBJEXT) \
+#	times.$(OBJEXT) \
+#	mcmc.$(OBJEXT) \
+#	rates.$(OBJEXT) \
+#	spr.$(OBJEXT) \
+#	m4.$(OBJEXT) \
+#	draw.$(OBJEXT) \
+#	stats.$(OBJEXT) \
+#	tiporder.$(OBJEXT)
+tiporder_OBJECTS = $(am_tiporder_OBJECTS)
+tiporder_DEPENDENCIES =
+DEFAULT_INCLUDES = -I. -I$(top_builddir)
+depcomp = $(SHELL) $(top_srcdir)/depcomp
+am__depfiles_maybe = depfiles
+am__mv = mv -f
+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
+	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+AM_V_CC = $(am__v_CC_$(V))
+am__v_CC_ = $(am__v_CC_$(AM_DEFAULT_VERBOSITY))
+am__v_CC_0 = @echo "  CC    " $@;
+AM_V_at = $(am__v_at_$(V))
+am__v_at_ = $(am__v_at_$(AM_DEFAULT_VERBOSITY))
+am__v_at_0 = @
+CCLD = $(CC)
+LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
+AM_V_CCLD = $(am__v_CCLD_$(V))
+am__v_CCLD_ = $(am__v_CCLD_$(AM_DEFAULT_VERBOSITY))
+am__v_CCLD_0 = @echo "  CCLD  " $@;
+AM_V_GEN = $(am__v_GEN_$(V))
+am__v_GEN_ = $(am__v_GEN_$(AM_DEFAULT_VERBOSITY))
+am__v_GEN_0 = @echo "  GEN   " $@;
+SOURCES = $(m4_SOURCES) $(part_SOURCES) $(phycont_SOURCES) \
+	$(phyml_SOURCES) $(phyml_mpi_SOURCES) $(phytime_SOURCES) \
+	$(rf_SOURCES) $(test_SOURCES) $(tiporder_SOURCES)
+DIST_SOURCES = $(am__m4_SOURCES_DIST) $(am__part_SOURCES_DIST) \
+	$(am__phycont_SOURCES_DIST) $(am__phyml_SOURCES_DIST) \
+	$(am__phyml_mpi_SOURCES_DIST) $(am__phytime_SOURCES_DIST) \
+	$(am__rf_SOURCES_DIST) $(am__test_SOURCES_DIST) \
+	$(am__tiporder_SOURCES_DIST)
+ETAGS = etags
+CTAGS = ctags
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ACLOCAL = ${SHELL} /home/guindon/Downloads/phyml-20120412/missing --run aclocal-1.11
+AMTAR = ${SHELL} /home/guindon/Downloads/phyml-20120412/missing --run tar
+AM_DEFAULT_VERBOSITY = 1
+AUTOCONF = ${SHELL} /home/guindon/Downloads/phyml-20120412/missing --run autoconf
+AUTOHEADER = ${SHELL} /home/guindon/Downloads/phyml-20120412/missing --run autoheader
+AUTOMAKE = ${SHELL} /home/guindon/Downloads/phyml-20120412/missing --run automake-1.11
+AWK = gawk
+CC = gcc
+CCDEPMODE = depmode=gcc3
+CFLAGS = -ansi -pedantic -Wall -std=c99 -O0 -g
+CPP = gcc -E
+CPPFLAGS = 
+CYGPATH_W = echo
+DEFS = $(REVISION)
+DEPDIR = .deps
+ECHO_C = 
+ECHO_N = -n
+ECHO_T = 
+EGREP = /usr/bin/grep -E
+EXEEXT = 
+GREP = /usr/bin/grep
+INSTALL = /usr/bin/install -c
+INSTALL_DATA = ${INSTALL} -m 644
+INSTALL_PROGRAM = ${INSTALL}
+INSTALL_SCRIPT = ${INSTALL}
+INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
+LDFLAGS = 
+LIBOBJS = 
+LIBS = -lm 
+LTLIBOBJS = 
+MAKEINFO = ${SHELL} /home/guindon/Downloads/phyml-20120412/missing --run makeinfo
+MKDIR_P = /usr/bin/mkdir -p
+OBJEXT = o
+PACKAGE = phyml
+PACKAGE_BUGREPORT = s.guindon@auckland.ac.nz
+PACKAGE_NAME = PhyML
+PACKAGE_STRING = PhyML 20120412
+PACKAGE_TARNAME = phyml
+PACKAGE_URL = 
+PACKAGE_VERSION = 20120412
+PATH_SEPARATOR = :
+SET_MAKE = 
+SHELL = /bin/sh
+STRIP = 
+VERSION = 20120412
+abs_builddir = /home/guindon/Downloads/phyml-20120412/src
+abs_srcdir = /home/guindon/Downloads/phyml-20120412/src
+abs_top_builddir = /home/guindon/Downloads/phyml-20120412
+abs_top_srcdir = /home/guindon/Downloads/phyml-20120412
+ac_ct_CC = gcc
+am__include = include
+am__leading_dot = .
+am__quote = 
+am__tar = ${AMTAR} chof - "$$tardir"
+am__untar = ${AMTAR} xf -
+bindir = ${exec_prefix}/bin
+build = x86_64-unknown-linux-gnu
+build_alias = 
+build_cpu = x86_64
+build_os = linux-gnu
+build_vendor = unknown
+builddir = .
+datadir = ${datarootdir}
+datarootdir = ${prefix}/share
+docdir = ${datarootdir}/doc/${PACKAGE_TARNAME}
+dvidir = ${docdir}
+exec_prefix = ${prefix}
+host = x86_64-unknown-linux-gnu
+host_alias = 
+host_cpu = x86_64
+host_os = linux-gnu
+host_vendor = unknown
+htmldir = ${docdir}
+includedir = ${prefix}/include
+infodir = ${datarootdir}/info
+install_sh = ${SHELL} /home/guindon/Downloads/phyml-20120412/install-sh
+libdir = ${exec_prefix}/lib
+libexecdir = ${exec_prefix}/libexec
+localedir = ${datarootdir}/locale
+localstatedir = ${prefix}/var
+mandir = ${datarootdir}/man
+mkdir_p = /usr/bin/mkdir -p
+oldincludedir = /usr/include
+pdfdir = ${docdir}
+prefix = /usr/local
+program_transform_name = s,x,x,
+psdir = ${docdir}
+sbindir = ${exec_prefix}/sbin
+sharedstatedir = ${prefix}/com
+srcdir = .
+sysconfdir = ${prefix}/etc
+target_alias = 
+top_build_prefix = ../
+top_builddir = ..
+top_srcdir = ..
+PROG = PHYML
+#PROG = TEST
+#PROG = PHYML
+#PROG = RF
+#PROG = M4
+#PROG = TIPORDER
+#PROG = RWRAP
+#PROG = PART
+#PROG = PHYCONT
+#PROG = PHYTIME
+#phytime_SOURCES = main.c \
+#utilities.c utilities.h\
+#optimiz.c optimiz.h\
+#lk.c lk.h\
+#bionj.c bionj.h\
+#models.c models.h\
+#free.c free.h\
+#help.c help.h\
+#simu.c simu.h\
+#eigen.c eigen.h\
+#pars.c pars.h\
+#alrt.c alrt.h\
+#interface.c interface.h\
+#cl.c cl.h\
+#spr.c spr.h\
+#times.c times.h\
+#m4.c m4.h\
+#draw.c draw.h\
+#rates.c rates.h\
+#mcmc.c mcmc.h\
+#stats.c stats.h\
+#mg.c mg.h\
+#tiporder.c tiporder.h
+
+#phytime_LDADD = -lm
+#phycont_SOURCES = main.c \
+#utilities.c utilities.h\
+#optimiz.c optimiz.h\
+#lk.c lk.h\
+#bionj.c bionj.h\
+#models.c models.h\
+#free.c free.h\
+#help.c help.h\
+#simu.c simu.h\
+#eigen.c eigen.h\
+#pars.c pars.h\
+#alrt.c alrt.h\
+#interface.c interface.h\
+#cl.c cl.h\
+#spr.c spr.h\
+#times.c times.h\
+#m4.c m4.h\
+#draw.c draw.h\
+#rates.c rates.h\
+#mcmc.c mcmc.h\
+#stats.c stats.h\
+#mg.c mg.h\
+#tiporder.c tiporder.h
+
+# continuous.c continuous.h
+#phycont_LDADD = -lm
+# if WANT_RWRAP
+# lib_LTLIBRARIES = librwrap.la
+# librwrap_la_SOURCES = main.c \
+# utilities.c utilities.h\
+# optimiz.c optimiz.h\
+# lk.c lk.h\
+# bionj.c bionj.h\
+# models.c models.h\
+# free.c free.h\
+# help.c help.h\
+# simu.c simu.h\
+# eigen.c eigen.h\
+# pars.c pars.h\
+# alrt.c alrt.h\
+# interface.c interface.h\
+# cl.c cl.h\
+# mg.c mg.h\
+# spr.c spr.h\
+# m4.c m4.h\
+# draw.c draw.h\
+# mcmc.c mcmc.h\
+# stats.c stats.h\
+# times.c times.h\
+# tiporder.c tiporder.h\
+# rates.c rates.h\
+# rwrapper.c rwrapper.h
+# librwrap_la_LIBADD = -lm
+# librwrap_la_LDFLAGS = -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -flat_namespace -undefined suppress -shared -module
+# librwrap_la_CFLAGS=-std=gnu99 -fPIC
+# else 
+#part_SOURCES = main.c \
+#utilities.c utilities.h\
+#optimiz.c optimiz.h\
+#lk.c lk.h\
+#bionj.c bionj.h\
+#models.c models.h\
+#free.c free.h\
+#help.c help.h\
+#simu.c simu.h\
+#eigen.c eigen.h\
+#pars.c pars.h\
+#alrt.c alrt.h\
+#interface.c interface.h\
+#cl.c cl.h\
+#mg.c mg.h\
+#spr.c spr.h\
+#m4.c m4.h\
+#draw.c draw.h\
+#stats.c stats.h\
+#tiporder.c tiporder.h
+
+#part_LDADD = -lm
+#tiporder_SOURCES = main.c \
+#utilities.c utilities.h\
+#optimiz.c optimiz.h\
+#lk.c lk.h\
+#bionj.c bionj.h\
+#models.c models.h\
+#free.c free.h\
+#help.c help.h\
+#simu.c simu.h\
+#eigen.c eigen.h\
+#pars.c pars.h\
+#alrt.c alrt.h\
+#interface.c interface.h\
+#cl.c cl.h\
+#mg.c mg.h\
+#times.c times.h\
+#mcmc.c mcmc.h\
+#rates.c rates.h\
+#spr.c spr.h\
+#m4.c m4.h\
+#draw.c draw.h\
+#stats.c stats.h\
+#tiporder.c tiporder.h
+
+#tiporder_LDADD = -lm
+#m4_SOURCES = main.c \
+#utilities.c utilities.h\
+#optimiz.c optimiz.h\
+#lk.c lk.h\
+#bionj.c bionj.h\
+#models.c models.h\
+#free.c free.h\
+#help.c help.h\
+#simu.c simu.h\
+#eigen.c eigen.h\
+#pars.c pars.h\
+#alrt.c alrt.h\
+#interface.c interface.h\
+#cl.c cl.h\
+#mg.c mg.h\
+#times.c times.h\
+#mcmc.c mcmc.h\
+#rates.c rates.h\
+#spr.c spr.h\
+#draw.c draw.h\
+#stats.c stats.h\
+#tiporder.c tiporder.h\
+#m4.c m4.h
+
+#m4_LDADD = -lm
+#rf_SOURCES = main.c \
+#utilities.c utilities.h\
+#optimiz.c optimiz.h\
+#lk.c lk.h\
+#bionj.c bionj.h\
+#models.c models.h\
+#free.c free.h\
+#help.c help.h\
+#simu.c simu.h\
+#eigen.c eigen.h\
+#pars.c pars.h\
+#alrt.c alrt.h\
+#interface.c interface.h\
+#cl.c cl.h\
+#mg.c mg.h\
+#times.c times.h\
+#mcmc.c mcmc.h\
+#rates.c rates.h\
+#spr.c spr.h\
+#draw.c draw.h\
+#stats.c stats.h\
+#tiporder.c tiporder.h\
+#m4.c m4.h
+
+#rf_LDADD = -lm
+#phyml_mpi_SOURCES = main.c \
+#utilities.c  utilities.h\
+#optimiz.c  optimiz.h\
+#lk.c  lk.h\
+#bionj.c bionj.h\
+#models.c  models.h\
+#free.c  free.h\
+#help.c  help.h\
+#simu.c  simu.h\
+#eigen.c  eigen.h\
+#pars.c  pars.h\
+#alrt.c  alrt.h\
+#interface.c  interface.h\
+#cl.c  cl.h\
+#spr.c spr.h\
+#draw.c  draw.h\
+#mpi_boot.c  mpi_boot.h\
+#stats.c stats.h\
+#rates.c rates.h\
+#mcmc.c mcmc.h\
+#times.c times.h\
+#tiporder.c tiporder.h\
+#mg.c mg.h\
+#m4.c m4.h\
+#xml.c xml.h
+
+#phyml_mpi_LDADD = -lm
+#test_SOURCES = main.c \
+#utilities.c  utilities.h\
+#optimiz.c  optimiz.h\
+#lk.c  lk.h\
+#bionj.c bionj.h\
+#models.c  models.h\
+#free.c  free.h\
+#help.c  help.h\
+#simu.c  simu.h\
+#eigen.c  eigen.h\
+#pars.c  pars.h\
+#alrt.c  alrt.h\
+#interface.c  interface.h\
+#cl.c  cl.h\
+#spr.c spr.h\
+#draw.c  draw.h\
+#stats.c stats.h\
+#rates.c rates.h\
+#mcmc.c mcmc.h\
+#times.c times.h\
+#tiporder.c tiporder.h\
+#mg.c mg.h\
+#m4.c m4.h\
+#xml.c xml.h
+
+#test_LDADD = -lm
+phyml_SOURCES = main.c \
+utilities.c  utilities.h\
+optimiz.c  optimiz.h\
+lk.c  lk.h\
+bionj.c bionj.h\
+models.c  models.h\
+free.c  free.h\
+help.c  help.h\
+simu.c  simu.h\
+eigen.c  eigen.h\
+pars.c  pars.h\
+alrt.c  alrt.h\
+interface.c  interface.h\
+cl.c  cl.h\
+spr.c spr.h\
+draw.c  draw.h\
+stats.c stats.h\
+rates.c rates.h\
+mcmc.c mcmc.h\
+times.c times.h\
+tiporder.c tiporder.h\
+mg.c mg.h\
+m4.c m4.h
+
+phyml_LDADD = -lm 
+all: all-am
+
+.SUFFIXES:
+.SUFFIXES: .c .o .obj
+$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
+	@for dep in $?; do \
+	  case '$(am__configure_deps)' in \
+	    *$$dep*) \
+	      ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+	        && { if test -f $@; then exit 0; else break; fi; }; \
+	      exit 1;; \
+	  esac; \
+	done; \
+	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign src/Makefile'; \
+	$(am__cd) $(top_srcdir) && \
+	  $(AUTOMAKE) --foreign src/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+	@case '$?' in \
+	  *config.status*) \
+	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+	  *) \
+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+	esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure:  $(am__configure_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
+	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
+install-binPROGRAMS: $(bin_PROGRAMS)
+	@$(NORMAL_INSTALL)
+	test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
+	@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
+	for p in $$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; \
+	done | \
+	sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+	    -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:
diff -uN ./phyml-20120412/src/mcmc.c ./phyml-20120412-new-bak/src/mcmc.c
--- ./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]);
diff -uN ./phyml-20120412/src/optimiz.c ./phyml-20120412-new-bak/src/optimiz.c
--- ./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)
diff -uN ./phyml-20120412/src/tree ./phyml-20120412-new-bak/src/tree
--- ./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
diff -uN ./phyml-20120412/src/utilities.c ./phyml-20120412-new-bak/src/utilities.c
--- ./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));
diff -uN ./phyml-20120412/src/utilities.h ./phyml-20120412-new-bak/src/utilities.h
--- ./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 *\/ */
 
 
 /*!********************************************************/