[Bioperl-l] problems with clustalw

[Sendu Bala]

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:
http://docs.bioperl.org/bioperl-live/Bio/SimpleAlign.html

For printing, you'll want to use AlignIO:
http://docs.bioperl.org/bioperl-live/Bio/AlignIO.html
For an example, see:
http://www.bioperl.org/wiki/HOWTO:SearchIO#Using_the_methods