#!/usr/bin/perl -w
use strict;
use Bio::AlignIO;
BEGIN {$ENV{TCOFFEEDIR} = 
       '/home/edward/MyBioTool/T-COFFEE_Ver1.37/bin/'; }
use Bio::Tools::Run::Alignment::TCoffee;

my @params = (
              '-outfile' => 'tcof.out',
              '-maxlen'  => '100'
          );
my $factory = Bio::Tools::Run::Alignment::TCoffee->new(@params);

my @array = qw( GGGTGTTATTCAAGCAAAAAAA
                TTTGGAAGTCAATATTTTGTCG
                CCTTTTATCTGTTTTGACAGTC
                ACTGAAAAGCTTAGGAAATGGT               
                TATTTGCAGTGATGTAATCAGC );

foreach  ( 0..$#array )
{
     push @seqs2, (Bio::Seq->new(-seq => $array[$_],  
                                 -display_id => 'seq_'.$_
                                )); 
} 

my  $seq_array_ref = \@seqs2;
my  $aln2 = $factory->align($seq_array_ref);  #final line that prints to STDOUT
 
__END__

##</code><code>##

....some text, followed by.....
T-COFFEE, Version_1.37 (Wed Jul 11 14:38:06 PDT 2001)
Notredame, Higgins, Heringa, JMB(302)pp205-217,2000
CPU   0 sec
SCORE 524          **Desired text to be captured
NSEQ  5
LEN   41

seq_1           ---TTTGGAAGTCAATATTTT------GTCG----------
seq_2           CCTTTTATCTG------TTTTGACA--GTC-----------
seq_3           -------ACTGAAAAGCTTAGGAAATGGT------------
seq_0           -------G-GG---------TGTTAT--TCAAGCAAAAAAA
seq_4           --TATTTGCAG---------TGATGTAATC-AGC-------
                          *                 *