biostars125994.pl - align all files in a directory

biostars125994.pl

#!/usr/bin/env perl

use strict;
use warnings;
use File::Find;
use Bio::Tools::Run::Alignment::Clustalw;

my $dir = 'genes';
my @files;
find( sub {
    push @files, $File::Find::name if -f and /\.fa$/
    }, $dir);

for my $file (@files) {
    my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM', 'outfile' => "$file.aln");
    my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
    my $aln = $factory->align($file);
    
    # do something with $aln
}