#!/usr/bin/perl -w
use strict;

# we want to consider various multiple alignment programs
# clustalw
# muscle
# tcoffee
# probcons
# mafft - good for VERY large families

use Bio::Tools::Run::Alignment::Muscle;
use Bio::Tools::Run::Alignment::TCoffee;
use Bio::Tools::Run::Alignment::Clustalw;
use Bio::AlignIO;

my $factory = Bio::Tools::Run::Alignment::Muscle->new;

my $dir = shift @ARGV || 'clusterfam';  
opendir(DIR, $dir) || die "cannot open dir $dir: $!";
for my $file ( readdir(DIR) ) {
  if( $file =~ /(\S+\.pep).fa$/ ) {
    my $stem = $1;
    my $aln = $factory->align("$dir/$file");
    my $out = Bio::AlignIO->new(-file => ">$dir/$stem.aln",
			       -format => 'fasta'); 
   $out->write_aln($aln);
  }
}