#!/usr/bin/env perl

use strict;
use warnings;

use Bio::Tools::Run::Alignment::Muscle;

# Build a muscle alignment factory
my @params = ( -outfile_name => 'outfile.fa' );
my $factory = Bio::Tools::Run::Alignment::Muscle->new(@params);

# Pass the factory a list of sequences to be aligned .
my $inputfilename = 'sequence.fa';

# $aln is a SimpleAlign object .
my $aln = $factory->align( $inputfilename );

exit;