[Bioperl-l] problems with clustalw

Sendu Bala bix at sendu.me.uk
Mon May 12 14:50:45 EDT 2008

vdar at yorku.ca wrote:
> Thanks a lot! You have solved the problem. I am getting the following output
> now. Would it be possible for you to let me know how can I print the
> alignments? I need the alignments as we get after running web-based clustalw or
> multalin programs.
>> Or just:
>> my $aln = $factory->align([$seq_obj_on, $seq_obj_too, $seq_obj_thre]);

$aln is a Bio::SimpleAlign object.
Check the docs for how to use it:

For printing, you'll want to use AlignIO:
For an example, see:

More information about the Bioperl-l mailing list