#!/usr/bin/perl
    $ENV{CLUSTALDIR} = 'C:\Program Files (x86)\ClustalW2';
    use warnings;
    use strict;
    
    use Bio::AlignIO;
    use Bio::SeqIO;
    use Bio::Tools::Run::Alignment::Clustalw;
    
    my $file = <>; # Get file name from command prompt.
    my $factory = Bio::Tools::Run::Alignment::Clustalw->new(-matrix => 'BLOSUM');
    my $ktuple = 3;
    $factory->ktuple($ktuple);
    
    my $inseq = Bio::SeqIO->new(
                        -file => "<$file",
                        -format => "fasta"
                       );
    
    my $seq;
    my @seq_array;
    while ($seq = $inseq->next_seq) {
        push(@seq_array, $seq);
    }
    
    # Now we do the actual alignment.
    my $seq_array_ref = \@seq_array;
    my $aln = $factory->align($seq_array_ref);