[Bioperl-l] Getting Alignment Score from Bio::Tools::Run::Alignment::TCoffee

Edward Wijaya ewijaya at singnet.com.sg
Wed Apr 20 05:26:56 EDT 2005

For the above TCoffee alignment module

Is there a way to:
1. get the alignment score (any method for this)
2. Pass input sequence as an array (not fasta file)
   e.g. input is "@seq = qw(ATCCGGA AGGGGAA)" etc.

Below is my current working program.

Thanks and hope to hear from you again.

#!/usr/bin/perl -w
use strict;
use Bio::AlignIO;
use Data::Dumper;

BEGIN {$ENV{TCOFFEEDIR} = '/home/edward/MyBioTool/T-COFFEE_distribution_Version_2.03/bin/'; }
use Bio::Tools::Run::Alignment::TCoffee;

my $inputfilename = "hm02r.fasta";
my $outfile = "tcoffee.out";
my @params = (
              '-in'    => $inputfilename,
              '-outfile' => $outfile,
my $factory = Bio::Tools::Run::Alignment::TCoffee->new(@params);
my $aln = $factory->align($inputfilename);


More information about the Bioperl-l mailing list