--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloconversion/fasta2phytab.pl	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,40 @@
+#!/usr/bin/perl -w
+
+use strict;
+
+use FindBin;
+use lib "$FindBin::Bin/lib";
+use Bio::DB::Fasta;
+use Bio::SeqIO;
+use Bio::Seq;
+
+#inputs
+my $infile=shift(@ARGV);
+my $species=shift(@ARGV);
+my $partition=shift(@ARGV);
+my $delpipes=shift(@ARGV);
+my $fromfasta;
+#for debugging xml input
+#print "$infile $species $partition $delpipes\n";
+#exit;
+
+if($species eq "from fasta"){
+	$fromfasta=1;
+}
+my $seqid;
+# open infile fasta file
+my $in_obj = Bio::SeqIO->new(-file => $infile, '-format' =>'fasta');
+
+#no warnings 'uninitialized';	#Was getting error on one fasta for uninitialized sequences. Never could track down why and used this as a workaround
+while (my $seq = $in_obj->next_seq() ) {
+	my $sequence = $seq->seq;
+	$seqid = $seq->id;
+	if($delpipes eq 'yes'){
+		$seqid =~ s/\|/_/g;
+	}
+	if($fromfasta){
+		$species = $seqid;
+	} 
+	$sequence =~ s/\n//g;
+	print $species."\t".$partition."\t".$seqid."\t".$sequence."\n";
+}