Version 20241207

stephaneguindon · Jul 12, 2024 · ccde895 · ccde895
1 parent efd0397
commit ccde895
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Showing 7 changed files with 17 additions and 10 deletions.
diff --git a/configure.ac b/configure.ac
@@ -1,7 +1,7 @@
 #                                               -*- Autoconf -*-
 # Process this file with autoconf to produce a configure script.
 
-AC_INIT([PhyML],esyscmd([sh -c "echo "3.3." | tr -d '\n' ; echo "20230824" | tr -d '\n'"]),[[email protected]])
+AC_INIT([PhyML],esyscmd([sh -c "echo "3.3." | tr -d '\n' ; echo "20241207" | tr -d '\n'"]),[stephane.[email protected]])
 AM_INIT_AUTOMAKE([foreign])
 AC_CONFIG_SRCDIR([src/main.c],[doc/phyml-manual.tex])
 AC_CONFIG_HEADERS([config.h])

diff --git a/src/init.c b/src/init.c
@@ -634,6 +634,7 @@ void Set_Defaults_Input(option* io)
   io->n_boot_replicates          = 0;
   io->print_mat_and_exit         = NO;
   io->edge_len_unit              = SUBSTITUTIONS;    
+
 
 #ifdef BEAGLE
   io->beagle_resource            = 0;

diff --git a/src/io.c b/src/io.c
@@ -2373,8 +2373,13 @@ void Print_Fp_Out(FILE *fp_out, time_t t_beg, time_t t_end, t_tree *tree, option
     }
   else
     {
-      fprintf(fp_out,"\n. Substitution model: \t\t\t%s",tree->mod->modelname->s);
+      PhyML_Fprintf(fp_out,"\n. Substitution model: \t\t%s",tree->mod->modelname->s);
     }
+
+  PhyML_Fprintf(fp_out,"\n. Integrated length (IL) model: \t%s",(tree->io->mod->gamma_mgf_bl == YES)?"yes":"no");
+
+  if(tree->io->mod->gamma_mgf_bl == YES) PhyML_Fprintf(fp_out,"\n. Variance of IL model: \t\t%.5f",tree->mod->l_var_sigma);
+
 
   PhyML_Fprintf(fp_out,"\n. Number of taxa: \t\t\t%d",tree->n_otu);/*added FLT*/
 
@@ -3125,7 +3130,7 @@ void Print_Banner(FILE *fp)
   PhyML_Fprintf(fp,"    A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood    \n");
   PhyML_Fprintf(fp,"                            Stephane Guindon & Olivier Gascuel                                      \n");
   PhyML_Fprintf(fp,"                                                                                                  \n");
-  PhyML_Fprintf(fp,"                           http://www.atgc-montpellier.fr/phyml                                          \n");
+  PhyML_Fprintf(fp,"                    https://github.com/stephaneguindon/phyml/tree/master                          \n");
   PhyML_Fprintf(fp,"                                                                                                  \n");
   PhyML_Fprintf(fp,"                         Copyright CNRS - Universite Montpellier                                  \n");
   PhyML_Fprintf(fp,"                                                                                                  \n");
@@ -3141,7 +3146,7 @@ void Print_Banner_Small(FILE *fp)
   PhyML_Fprintf(fp,"\n");
   PhyML_Fprintf(fp," oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo\n");
   PhyML_Fprintf(fp,"                                  ---  PhyML %s  ---                                             \n",VERSION);
-  PhyML_Fprintf(fp,"                              http://www.atgc-montpellier.fr/phyml                                          \n");
+  PhyML_Fprintf(fp,"                       https://github.com/stephaneguindon/phyml/tree/master                      \n");
   PhyML_Fprintf(fp,"                             Copyright CNRS - Universite Montpellier                                 \n");
   PhyML_Fprintf(fp," oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo\n");
 }

diff --git a/src/lk.c b/src/lk.c
@@ -691,7 +691,8 @@ phydbl dLk(phydbl *l, t_edge *b, t_tree *tree)
       rr *=  tree->mod->br_len_mult->v;      
 
       len = (*l) * rr;
-      var = tree->mod->l_var_sigma * rr*rr;
+      /* var = tree->mod->l_var_sigma * rr*rr; */
+      var = (*l) * tree->mod->l_var_sigma * rr*rr;
 
       if(isinf(len) || isnan(len)) 
         {
@@ -2234,7 +2235,8 @@ void Update_PMat_At_Given_Edge(t_edge *b_fcus, t_tree *tree)
 
           mean = len;
           /* var  = MAX(0.0,b_fcus->l_var->v) * POW(tree->mod->ras->gamma_rr->v[i]*tree->mod->br_len_mult->v,2); */
-          var  = tree->mod->l_var_sigma * POW(tree->mod->ras->gamma_rr->v[i]*tree->mod->br_len_mult->v,2);
+          /* var  = tree->mod->l_var_sigma * POW(tree->mod->ras->gamma_rr->v[i]*tree->mod->br_len_mult->v,2); */
+          var  = MAX(0.0,b_fcus->l->v) * tree->mod->l_var_sigma * POW(tree->mod->ras->gamma_rr->v[i]*tree->mod->br_len_mult->v,2);
           if(tree->mixt_tree) var *= POW(tree->mixt_tree->mod->ras->gamma_rr->v[tree->mod->ras->parent_class_number],2);
 
           /* var = 1.E-10; */

diff --git a/src/main.c b/src/main.c
@@ -267,7 +267,7 @@ int main(int argc, char **argv)
                     }
 
 
-                  if(tree->mod->gamma_mgf_bl) Best_Root_Position_IL_Model(tree);
+                  /* if(tree->mod->gamma_mgf_bl) Best_Root_Position_IL_Model(tree); */
 
                   Set_Both_Sides(YES,tree);
                   Lk(NULL,tree);
@@ -280,8 +280,7 @@ int main(int argc, char **argv)
                   Check_Br_Lens(tree);
                   Br_Len_Involving_Invar(tree);
                   Rescale_Br_Len_Multiplier_Tree(tree);
-
-
+
 #elif defined EVOLVE
                   Evolve(tree->data,tree->mod,tree);
                   Exit("\n. Exiting 'evolve'\n");

diff --git a/src/utilities.c b/src/utilities.c
@@ -10506,7 +10506,6 @@ void Best_Root_Position_IL_Model(t_tree *tree)
           Set_Both_Sides(YES,tree);
           Lk(NULL,tree);
           /* Optimize_Br_Len_Serie(2,tree); */
-          PhyML_Printf("\n HERE");
 
           Update_Partial_Lk(tree,tree->n_root->b[1],tree->n_root);
           Br_Len_Opt(&(tree->n_root->b[1]->l->v),tree->n_root->b[1],tree);

diff --git a/src/utilities.h b/src/utilities.h
@@ -929,6 +929,7 @@ typedef struct __Tree{
 
   int n_edges_traversed;
   int n_tot_bl_opt;
+
 }t_tree;
 
 /*!********************************************************/