[Bioperl-l] Cannot read in alignment data with Bio::AlignIO

manni122 markus.liebscher at gmx.de
Tue Feb 10 09:40:49 EST 2009

I am trying to read in a file with multiple pairwise alignments. Some IDs
appear frequently. So if I am using this code below I get the error message:
--- MSG: Replacing one sequence xxx ---
Is there a way to read the data even with those similar names? 
Regards, manni122.

use Bio::AlignIO;

my $in  = Bio::AlignIO->new(-file => "align.fas" ,
                           -format => 'fasta');

my $aln = $in->next_result();

foreach my $seqObj ($aln->each_seq) {
  print $seqObj->display_id, "\n";

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