[Bioperl-l] Inconsistency in Alignment Score from Bio::Tools::Run::Alignment::TCoffee versus actual command-line program

[Edward WIJAYA]

Hi,

Below was my code that does the alignment for two sequences.
But how come it gives different result compare to the actual  
command-line/web result?
Zero versus 100  (note the * marked line)

Could it be a bug in the module?

---BioPerl Result----
PAIRWISE_ALIGNMENT [No Tree]
T-COFFEE, Version_2.03(Wed Jul 11 14:38:06 PDT 2001)
Notredame, Higgins, Heringa, JMB(302)pp205-217,2000
CPU   0 sec
SCORE 0          *
NSEQ  2
LEN   15

seq_0           AAAAAAAAAAAAAAA
seq_1           AAAAAAAAAAAAAAA
                 ***************

=VERSUS=

---Command Line Result---
									   *
CLUSTAL FORMAT for T-COFFEE Version_2.03, CPU=0.00 sec, SCORE=100, Nseq=2,  
Len=15

seq_0           AAAAAAAAAAAAAAA
seq_1           AAAAAAAAAAAAAAA
                 ***************

---Web Result--
http://www.ch.embnet.org/wwwtmp/run_2316.html



__BEGIN__
#!/usr/bin/perl -w
use strict;
use Bio::AlignIO;
BEGIN {$ENV{TCOFFEEDIR} =
        '/home/edward/MyBioTool/T-COFFEE_Ver2.03/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 (AAAAAAAAAAAAAAAA
                  AAAAAAAAAAAAAAAA);

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__

--
Regards,
Edward WIJAYA
SINGAPORE