--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloconversion/beautify_fasta.pl	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,50 @@
+#!/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 $outfile=shift(@ARGV);
+my $delpipes=shift(@ARGV);
+my $convgi=shift(@ARGV);
+my $delslash=shift(@ARGV);
+my $renumber=shift(@ARGV);
+my $space=shift(@ARGV);
+
+my $seqid;
+my $newnumbers=1; 		#for sequential renumbering of header
+# open infile fasta file
+my $in_obj = Bio::SeqIO->new(-file => $infile, '-format' =>'fasta');
+open FILE, ">$outfile" or die $!;
+
+while (my $seq = $in_obj->next_seq() ) {
+	my $sequence = $seq->seq;
+	$seqid = $seq->id;
+
+	if($delslash eq 'yes'){
+		$seqid =~ s/\\/_/g;
+	}
+	if($convgi eq 'yes'){
+		$seqid =~ s/gi\|/gi_/g;
+	}
+	if($delpipes eq 'yes'){
+		$seqid =~ s/\|/ /g;
+	}
+	$sequence =~ s/\n//g;
+	$sequence =~ tr/a-z/A-Z/;
+	print FILE ">";
+	if($renumber eq 'yes'){
+		print FILE $newnumbers;
+		if($space eq 'yes'){
+			print FILE " ";
+		}
+		$newnumbers++;
+	}
+	print FILE $seqid." ".$seq->desc."\n".$sequence."\n";
+}