--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alignment/fasconcat.pl	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,37 @@
+#!/usr/bin/perl
+
+use strict;
+
+my $fasconcatPath = '/home/galaxy/galaxy_dist/tools/fasconcat/FASconCAT_v1.0.pl';
+
+my $outputFormat = $ARGV[0];
+my $limit = $ARGV[1];
+my $outFormat;
+my @inputFiles;
+
+for(my $i = 2; $i <= $limit; $i++) {
+	$inputFiles[$i] = " -f ";
+	$inputFiles[$i] = $inputFiles[$i].$ARGV[$i];
+}
+
+if($outputFormat == "0") {
+	$outFormat = "";
+}
+elsif($outputFormat == "1") {
+	$outFormat = " -p -p";
+}
+else {
+	$outFormat = " -n -n";
+}
+
+my $run = qx/$fasconcatPath -s -i "@inputfiles" $outFormat /;
+
+if($outputFormat == "0") {
+	qx/cp FcC_smatrix.fas output/;
+}
+elsif($outputFormat == "1") {
+	qx/cp FcC_smatrix.phy output/;
+}
+else {
+	qx/cp FcC_smatrix.nex output/;
+}