[Bioperl-l] problems with clustalw

vdar at yorku.ca vdar at yorku.ca
Mon May 12 16:19:37 EDT 2008


Thank you so much!

Nisa

Quoting Sendu Bala <bix at sendu.me.uk>:

> 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
>
>




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