From 197c7c52db4a7f783380c22e7091719198a694ab Mon Sep 17 00:00:00 2001
From: stamatak <Alexandros.Stamatakis@gmail.com>
Date: Wed, 28 Jun 2017 10:39:42 +0200
Subject: [PATCH] fixed tree output in IC computation with partial gene trees

---
 README            | 2 +-
 axml.c            | 3 ++-
 axml.h            | 6 +++---
 bipartitionList.c | 2 +-
 models.c          | 2 +-
 treeIO.c          | 4 ++--
 6 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/README b/README
index 40428eb..1da33d0 100644
--- a/README
+++ b/README
@@ -1,4 +1,4 @@
-Standard RAxML version 8.2.10
+Standard RAxML version 8.2.11
 
 ============================================================================================================
 
diff --git a/axml.c b/axml.c
index 0482cb2..eaa7f7f 100644
--- a/axml.c
+++ b/axml.c
@@ -7887,7 +7887,8 @@ void printBipartitionResult(tree *tr, analdef *adef, boolean finalPrint, boolean
 	  fprintf(logFile, "%s", tr->tree_string);
 	  fclose(logFile);
 	}
-
+      
+     
       Tree2String(tr->tree_string, tr, tr->start->back, FALSE, TRUE, FALSE, FALSE, finalPrint, adef, NO_BRANCHES, TRUE, FALSE, printIC, FALSE);
       
       
diff --git a/axml.h b/axml.h
index 2465a8b..bfeaa03 100644
--- a/axml.h
+++ b/axml.h
@@ -168,9 +168,9 @@
 #define PointGamma(prob,alpha,beta)  PointChi2(prob,2.0*(alpha))/(2.0*(beta))
 
 #define programName        "RAxML"
-#define programVersion     "8.2.10"
-#define programVersionInt   8210
-#define programDate        "March 2017"
+#define programVersion     "8.2.11"
+#define programVersionInt   8211
+#define programDate        "June 2017"
 
 
 #define  TREE_EVALUATION                 0
diff --git a/bipartitionList.c b/bipartitionList.c
index f17930f..333b7c1 100644
--- a/bipartitionList.c
+++ b/bipartitionList.c
@@ -1833,7 +1833,7 @@ void calcBipartitions_IC_Global(tree *tr, analdef *adef, char *bestTreeFileName,
 {
   int    
     numberOfTrees,
-    numberOfTaxa = readSingleTree(tr, bestTreeFileName, adef, FALSE, FALSE, TRUE);
+    numberOfTaxa = readSingleTree(tr, bestTreeFileName, adef, TRUE, FALSE, TRUE);
 
   FILE 
     *treeFile; 
diff --git a/models.c b/models.c
index 49322b7..dfc3768 100644
--- a/models.c
+++ b/models.c
@@ -4118,7 +4118,7 @@ void makeGammaCats(int rateHetModel, double alpha, double *gammaRates, int K, bo
       for (i = 0; i < K; i++)
         gammaRates[i] *= scaler;
     }
-   
+     
 
   rax_free(gammaProbs);
 
diff --git a/treeIO.c b/treeIO.c
index a9ded68..5176f21 100644
--- a/treeIO.c
+++ b/treeIO.c
@@ -1103,8 +1103,8 @@ static boolean addElementLen (FILE *fp, tree *tr, nodeptr p, boolean readBranchL
     }
   else 
     {   
-      ungetc(ch, fp);
-      if ((n = treeFindTipName(fp, tr, TRUE)) <= 0)          return FALSE;
+      ungetc(ch, fp);    
+      if ((n = treeFindTipName(fp, tr, TRUE)) <= 0)          return FALSE;     
       q = tr->nodep[n];
       if (tr->start->number > n)  tr->start = q;
       (tr->ntips)++;