--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloconversion/gb2phytab.pl	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,41 @@
+#!/usr/bin/perl -w
+use strict;
+
+use Bio::SeqIO;
+
+
+my $datafile = $ARGV[0];
+my $outfile = $ARGV[1];
+
+open FILE, ">$outfile" or die "Cannot Write File\n"; 
+
+my $seqio_object = Bio::SeqIO->new(-file => $datafile,'-format' => 'genbank');
+
+while(my $seq_object = $seqio_object->next_seq){
+	my $organism = $seq_object->species->binomial();
+	$organism =~ s/ /_/g;
+	my $accession = $seq_object->id;
+	for my $feat_object ($seq_object->get_SeqFeatures) {
+	   if ($feat_object->primary_tag eq "CDS") {
+	      my $sequence = $feat_object->spliced_seq->seq;
+	      	if ($feat_object->has_tag('gene')) {
+			for my $name ($feat_object->get_tag_values('product')){
+				$name =~ s/ /_/g;
+				print FILE $organism."\t".$name."\t".$accession."\t".$sequence."\n";
+         		}
+		}
+	   }elsif ($feat_object->primary_tag eq "misc_RNA") {
+	      my $sequence = $feat_object->spliced_seq->seq;
+	      	if ($feat_object->has_tag('product')) {
+			for my $name ($feat_object->get_tag_values('product')){
+				$name =~ s/ /_/g;
+				print FILE $organism."\t".$name."\t".$accession."\t".$sequence."\n";
+         		}
+		}
+   	   }
+
+	}
+}
+close FILE;
+
+