[Bioperl-l] Generating a consensus sequence from a Clustal alignment

Bill Stephens grapeguy at gmail.com
Mon Oct 18 09:58:24 EDT 2010


All,

I'm in my first week with bioperl for a class project (although I've used
Perl for years). I've successfully run a clustal alignment of several DNA
sequences to produce the aln and dnd files. Now I would like to generate a
consensus sequence from the alignment.  I see that Pise Cons does this
satisfactorily on my example data (
http://mobyle.pasteur.fr/cgi-bin/portal.py?form=consensus) . However, I'm
not finding Bio::Tools::Run::PiseApplication::cons in the 1.6.1 distribution
that I installed.

Is this another module that I need to install separately?

"cpan[2]> m /Pise/
Module    Bio::Tools::Run::AnalysisFactory::Pise
(BIRNEY/bioperl-run-1.4.tar.gz)
Module    Bio::Tools::Run::PiseApplication (BIRNEY/bioperl-run-1.4.tar.gz)"

Bill S.


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