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fixed a inconsistency in ProteinModelSelection.pl

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stamatak committed Oct 8, 2012
1 parent f9b87f0 commit 3917c6ffd763caca76151b08781f5ce3259fd938
Showing with 4 additions and 4 deletions.
  1. +3 −3 ProteinModelSelection.pl
  2. +1 −1 Release-Notes
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@@ -60,7 +60,7 @@ sub getTIME
{
print "Splitting up multi-gene alignment\n";
$partition = $ARGV[1];
- $cmd = $raxmlExecutable." -f s -m PROTCATJTT -O -p 12345 -s ".$alignmentName." -q ".$partition." -n SPLIT_".$alignmentName." \> SPLIT_".$alignmentName."_out";
+ $cmd = $raxmlExecutable." -f s -m PROTCATJTT -p 12345 -s ".$alignmentName." -q ".$partition." -n SPLIT_".$alignmentName." \> SPLIT_".$alignmentName."_out";
system($cmd);
$count = 0;
while(open(CPF, $alignmentName.".GENE.".$count))
@@ -76,15 +76,15 @@ sub getTIME
{
#print "Determining AA model data\n";
#print "Computing randomized stepwise addition starting tree number :".$i."\n";
- $cmd = $raxmlExecutable." -O -y -p 12345 -m PROTCATJTT -s ".$alignmentName." -n ST_".$alignmentName." \> ST_".$alignmentName."_out";
+ $cmd = $raxmlExecutable." -y -p 12345 -m PROTCATJTT -s ".$alignmentName." -n ST_".$alignmentName." \> ST_".$alignmentName."_out";
system($cmd);
$numberOfModels = @AA_Models;
for($i = 0; $i < $numberOfModels; $i++)
{
$aa = "PROTGAMMA".$AA_Models[$i];
- $cmd = $raxmlExecutable." -O -f e -m ".$aa." -s ".$alignmentName." -t RAxML_parsimonyTree.ST_".$alignmentName." -n ".$AA_Models[$i]."_".$alignmentName."_EVAL \> ".$AA_Models[$i]."_".$alignmentName."_EVAL.out\n";
+ $cmd = $raxmlExecutable." -f e -m ".$aa." -s ".$alignmentName." -t RAxML_parsimonyTree.ST_".$alignmentName." -n ".$AA_Models[$i]."_".$alignmentName."_EVAL \> ".$AA_Models[$i]."_".$alignmentName."_EVAL.out\n";
#print($cmd);
system($cmd);
}
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@@ -1,4 +1,4 @@
-RAxML v7.3.4
+RAxML v7.3.5
We view RAxML code development as permanent work in progress.

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