#!/usr/bin/env perl   


use Bio::AlignIO;
use strict;
use warnings;
use Data::Dumper;


my $inFi = $ARGV[0];
my $outFi = $ARGV[1];

my $stream  = Bio::AlignIO->new(-format => 'stockholm', -file => $inFi);
my $out = Bio::AlignIO->new(-file => ">$outFi", -format => 'clustalw');

while ( my $aln = $stream->next_aln ) {
  $out->write_aln($aln); 
}
