--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Rooting/Rooting.pl	Wed Feb 07 22:08:47 2018 -0500
@@ -0,0 +1,58 @@
+#!/usr/bin/perl
+
+use strict;
+use Getopt::Long;
+use Bio::SeqIO;
+use Cwd ;
+use FindBin qw ( $Bin $Script );
+
+my $CURRENT_DIR = $Bin;
+
+my $ROOTING_EXE = "java -jar ". $CURRENT_DIR . "/Rootings_54.jar";
+
+my $usage = qq~Usage:$0 <args> [<opts>]
+where <args> are:
+    -i, --input         <newick input>
+    -o, --output        <newick output>
+~;
+$usage .= "\n";
+
+my ($input,$outfile);
+
+
+GetOptions(
+	"input=s"    => \$input,
+	"output=s"   => \$outfile
+);
+
+
+die $usage
+  if ( !$input || !$outfile);
+  
+my $treefile = $input;
+	
+
+# replace negative values by 0
+open(T,$treefile);
+open(T2,">$treefile.2");
+while(<T>)
+{
+	my $line = $_;
+	$line =~s/\-\d+\.*\d*\,/0,/g;
+	$line =~s/\-\d+\.*\d*\)/0\)/g;
+	print T2 $line;
+}
+close(T);
+close(T2);
+	
+my $rooting_command = $ROOTING_EXE . " -input $treefile.2 -output $treefile.all -midpoint $treefile.midpoint >>$treefile.rooting.log 2>&1";
+system($rooting_command);
+
+unlink("$treefile.all");
+unlink("$treefile.2");
+rename("$treefile.midpoint",$outfile);
+
+	
+	
+
+