--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloconversion/remove_gbs_dupes.pl	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,43 @@
+#!/usr/bin/perl -w
+use strict;
+
+my $datafile = $ARGV[0];
+my $keepfile = $ARGV[1];
+my $delfile = $ARGV[2];
+my $subsp = $ARGV[3];
+my $var = $ARGV[4];
+
+open (FILE,"<$datafile") or die "Cannot open file input file\n";
+open (KFILE,">$keepfile") or die "Cannot open file $keepfile\n";
+open (DFILE,">$delfile") or die "Cannot open file delfile\n";
+
+my $keep = 1;
+
+while (<FILE>)
+{
+	if($_ =~ m/_\d/){
+		$keep=0;
+	}else{
+		if($subsp==1){
+			if($_ =~ m/subsp/){
+				$keep=0;
+			}
+		}
+		if($var==1){
+			if($_ =~ m/_var_/){
+				$keep=0;
+			}
+		}
+	}
+
+	if($keep == 0){
+		print DFILE $_;
+	}else{
+		print KFILE $_;
+	}
+	$keep=1; #reset variable. Default is keep
+}
+close FILE;
+close KFILE;
+close DFILE;
+