#!/ usr/bin/ perl
use strict;
use warnings;
use Bio::Tools::Run::Alignment::Muscle;
# Build a muscle alignment factory
my $factory =Bio::Tools::Run::Alignment::Muscle -> new(@params );
# Pass the factory a list of sequences to be aligned .
my $inputfilename = 'sequence.fasta ';
# $aln is a SimpleAlign object .
my $aln = $factory -> align ( $inputfilename );
# Perform a profile alignment on a MSA to include more seqs
my $alnfilename = 'sequence.fasta ';
my $seqsfilename = 'outfile ';
$aln = $factory -> profile ( $alnfilename , $seqsfilename );