[med-svn] [raxml] 01/06: New upstream version 8.2.10+dfsg

[Andreas Tille]

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tille pushed a commit to branch master
in repository raxml.

commit 3249a50913be72e2c5eef160185ab216ef46530c
Author: Andreas Tille <tille at debian.org>
Date:   Sat Jun 24 06:17:58 2017 +0200

    New upstream version 8.2.10+dfsg
---
 README               |   2 +-
 axml.c               |   8 ++++----
 axml.h               |   6 +++---
 manual/NewManual.odt | Bin 136886 -> 137089 bytes
 manual/NewManual.pdf | Bin 634532 -> 634890 bytes
 optimizeModel.c      |   5 +++--
 6 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/README b/README
index 46561bc..40428eb 100644
--- a/README
+++ b/README
@@ -1,4 +1,4 @@
-Standard RAxML version 8.2.9
+Standard RAxML version 8.2.10
 
 ============================================================================================================
 
diff --git a/axml.c b/axml.c
index 7a66fba..0482cb2 100644
--- a/axml.c
+++ b/axml.c
@@ -4882,11 +4882,11 @@ static void printMinusFUsage(void)
 
   printf("              \"-f F\": execute fast experimental tree search, at present only for testing\n");
 
-  printf("              \"-f g\": compute per site log Likelihoods for one ore more trees passed via\n");
+  printf("              \"-f g\": compute per site log Likelihoods for one or more trees passed via\n");
   printf("                      \"-z\" and write them to a file that can be read by CONSEL\n");
   printf("                      The model parameters will be estimated on the first tree only!\n");
   
-  printf("              \"-f G\": compute per site log Likelihoods for one ore more trees passed via\n");
+  printf("              \"-f G\": compute per site log Likelihoods for one or more trees passed via\n");
   printf("                      \"-z\" and write them to a file that can be read by CONSEL.\n");
   printf("                      The model parameters will be re-estimated for each tree\n");
  
@@ -7599,7 +7599,7 @@ static void printModelAndProgramInfo(tree *tr, analdef *adef, int argc, char *ar
 
 	  
 	  if(tr->rateHetModel == GAMMA || tr->rateHetModel == GAMMA_I)
-	    printBoth(infoFile, "%s model of rate heteorgeneity, ML estimate of alpha-parameter\n\n", modelType);
+	    printBoth(infoFile, "%s model of rate heterogeneity, ML estimate of alpha-parameter\n\n", modelType);
 	  else
 	    {
 	      printBoth(infoFile, "ML estimate of %d per site rate categories\n\n", adef->categories);
@@ -13330,7 +13330,7 @@ static void checkAscBias(tree *tr)
 	  {
 	    printBothOpen("\nWARNING: you specified that you want to use an ascertainment bias correction for partition %d\n", model);
 	    printBothOpen("for the CAT model of rate heterogeneity. Are you sure that you don't want to use a model without any rate \n");
-	    printBothOpen("heteorgeneity modeling via the \"-V\" command line switch?\n");
+	    printBothOpen("heterogeneity modeling via the \"-V\" command line switch?\n");
 	  }
       }
 }
diff --git a/axml.h b/axml.h
index b5e4799..2465a8b 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     "8.2.9"
-#define programVersionInt   8290
-#define programDate        "July 20 2016"
+#define programVersion     "8.2.10"
+#define programVersionInt   8210
+#define programDate        "March 2017"
 
 
 #define  TREE_EVALUATION                 0
diff --git a/manual/NewManual.odt b/manual/NewManual.odt
index e3ed9fe..e74abd7 100644
Binary files a/manual/NewManual.odt and b/manual/NewManual.odt differ
diff --git a/manual/NewManual.pdf b/manual/NewManual.pdf
index 81214d7..aeabc47 100644
Binary files a/manual/NewManual.pdf and b/manual/NewManual.pdf differ
diff --git a/optimizeModel.c b/optimizeModel.c
index 05fcac6..96e1ac6 100644
--- a/optimizeModel.c
+++ b/optimizeModel.c
@@ -4218,8 +4218,9 @@ static boolean optimizeRatesBFGS(tree *tr)
 	  bound_check_GTR[i] = FALSE;
 	  //added this max here to prevent num problems when the boundary value is set lower than 
 	  //the error margin!
-	  lowerGTR[i] = MAX(RATE_MIN, ERROR_X);
-	  upperGTR[i] = RATE_MAX;
+	  lowerGTR[i] = MAX(RATE_MIN + RATE_MIN * ERROR_X, ERROR_X);
+	  upperGTR[i] = RATE_MAX - RATE_MAX * ERROR_X;
+	  //printf("%1.20f %1.20f %1.20f %1.20f\n", lowerGTR[i], upperGTR[i], RATE_MIN, RATE_MAX);
 	}
     }
 

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