From e43719c25b8eb55fb9c4f86274c449a16eb2f1ac Mon Sep 17 00:00:00 2001
From: Stephane Guindon <stephane.guindon@gmail.com>
Date: Wed, 14 Aug 2024 12:09:36 +0200
Subject: [PATCH] Fixed bug in reading (and printing) bootstrap support values

---
 src/io.c        | 24 +++++++++++++++++-------
 src/main.c      |  2 +-
 src/nexus.c     |  6 ++++--
 src/utilities.c |  4 ++--
 4 files changed, 24 insertions(+), 12 deletions(-)

diff --git a/src/io.c b/src/io.c
index 09b21544..b18d654c 100644
--- a/src/io.c
+++ b/src/io.c
@@ -351,11 +351,21 @@ void Read_Branch_Support(char *s_d, char *s_a, t_edge *b, t_tree *tree)
   p++;
 
   i = 0;
-  if(p[i] == '(') i = Next_Matching_Char(p,'(',')',i);
-  i++;  
-  if(p[i] == '[') i = Next_Matching_Char(p,'[',']',i);
-  i++;
-  if(p[i] != ':') b->support_val = atof((char *)p);
+  if(p[i] == '(')
+    {
+      i = Next_Matching_Char(p,'(',')',i);
+      i++;
+    }
+  if(p[i] == '[')
+    {
+      i = Next_Matching_Char(p,'[',']',i);
+      i++;
+    }
+  
+  if(p[i] != ':')
+    {
+      b->support_val = atof((char *)(p+i));
+    }
     
   Free(sub_tp);
 }
@@ -6222,12 +6232,12 @@ void Collect_Edge_Support_Values(t_tree *tree)
     {      
       if(tree->io->do_boot == YES)
         {
-          tree->a_edges[i]->support_val = tree->a_edges[i]->bip_score; 
+          tree->a_edges[i]->support_val = (phydbl)tree->a_edges[i]->bip_score;
         }
       else if(tree->io->do_tbe == YES)
         {
           int pminus1=MIN(tree->a_edges[i]->left->bip_size[tree->a_edges[i]->l_r], tree->a_edges[i]->rght->bip_size[tree->a_edges[i]->r_l])-1;
-          tree->a_edges[i]->support_val = 1-((tree->a_edges[i]->tdist_score)/(tree->io->n_boot_replicates*1.0))/pminus1;
+          tree->a_edges[i]->support_val = 1.-((tree->a_edges[i]->tdist_score)/(tree->io->n_boot_replicates*1.0))/pminus1;
         }
       else if(tree->io->do_alrt == YES)
         {
diff --git a/src/main.c b/src/main.c
index 9f226a57..9dca7347 100644
--- a/src/main.c
+++ b/src/main.c
@@ -366,7 +366,7 @@ int main(int argc, char **argv)
               /* Print the most likely tree in the output file */
               if(!io->quiet) PhyML_Printf("\n\n. Printing the most likely tree in file '%s'.", Basename(io->out_tree_file));
               if(io->n_data_sets == 1) rewind(io->fp_out_tree);
-              
+
               t_tree *dum;
               dum = Read_Tree(&most_likely_tree);
               dum->data = cdata;
diff --git a/src/nexus.c b/src/nexus.c
index eb9ba137..22976d9d 100644
--- a/src/nexus.c
+++ b/src/nexus.c
@@ -267,12 +267,14 @@ int Read_Nexus_Format(char *token, nexparm *curr_parm, option *io)
 	{
 	  io->datatype = NT;
 	  io->mod->ns = 4;
+	  io->mod->whichmodel = HKY85;
 	}
 
       else if(!strcmp(curr_parm->value,"protein"))
 	{
 	  io->datatype = AA;
 	  io->mod->ns = 20;
+	  io->mod->whichmodel = LG;
 	}
       
       else if(!strcmp(curr_parm->value,"continuous"))
@@ -288,7 +290,7 @@ int Read_Nexus_Format(char *token, nexparm *curr_parm, option *io)
       PhyML_Printf("\n== The 'missing' subcommand is not supported by PhyML. Please remove it from the NEXUS file.");
       PhyML_Printf("\n== Note that the characters 'X', '?' and '-' will be considered as indels by default."); 
       PhyML_Printf("\n== Err. in file %s at line %d\n",__FILE__,__LINE__);
-      Exit("");
+      /* Exit(""); */
     }
 
   else if(!strcmp(curr_parm->name,"gap"))
@@ -296,7 +298,7 @@ int Read_Nexus_Format(char *token, nexparm *curr_parm, option *io)
       PhyML_Printf("\n== The 'gap' subcommand is not supported by PhyML. Please remove it from the NEXUS file.");
       PhyML_Printf("\n== Note that the characters 'X', '?' and '-' will be considered as indels by default."); 
       PhyML_Printf("\n== Err. in file %s at line %d\n",__FILE__,__LINE__);
-      Exit("");
+      /* Exit(""); */
     }
 
   else if(!strcmp(curr_parm->name,"symbols"))
diff --git a/src/utilities.c b/src/utilities.c
index dc94178b..984fa884 100644
--- a/src/utilities.c
+++ b/src/utilities.c
@@ -3277,6 +3277,7 @@ void Bootstrap(t_tree *tree)
       else if(tree->io->do_tbe) Compare_Bip_Distance(tree, boot_tree);
       else assert(FALSE);
 
+      
       Check_Br_Lens(boot_tree);
       Br_Len_Involving_Invar(boot_tree);
 
@@ -3330,7 +3331,7 @@ void Br_Len_Involving_Invar(t_tree *tree)
       return;
     }
 
-  For(i,2*tree->n_otu-1) tree->a_edges[i]->l->v *= (1.0-tree->mod->ras->pinvar->v);
+  for(i=0;i<2*tree->n_otu-1;++i) tree->a_edges[i]->l->v *= (1.0-tree->mod->ras->pinvar->v);
 }
 
 //////////////////////////////////////////////////////////////
@@ -4226,7 +4227,6 @@ int Compare_Bip(t_tree *tree1, t_tree *tree2, int on_existing_edges_only)
         }
     out: ;
     }
-
   return n_edges - identical;
 }