[Bioperl-l] Fwd: purge method of Bio::Align::AlignI

[Jason Stajich]

Laura - please ask these questions on the mailing list in the future  
so that others can benefit from the Q&A (and others can 'Answer').

It is indeed implemented in Bio::SimpleAlign - which is what you get  
back when you read in an alignment with Bio::AlignIO.
Bio::Align::AlignI is just an interface and not intended to be used  
directly.

-jason
Begin forwarded message:

> From: "Laura Wegener Parfrey" <lwegener at nsm.umass.edu>
> Date: December 9, 2008 10:46:19 AM PST
> To: jason at bioperl.org
> Subject: purge method of Bio::Align::AlignI
> Reply-To: lwegener at nsm.umass.edu
>
> I want to remove sequences that are similar to each other from an
> alignment.  I would like to use Bio::Align::AlignI 'purge' ,  but it  
> is not
> implemented.
>
> Is 'purge' implemented anywhere to do this? Or are there alternative
> methods?
> Thank you,
> Laura
>
> -- 
> Laura Wegener Parfrey
> Program in Organismic and Evolutionary Biology
> University of Massachusetts
> 611 N. Pleasant Street
> Amherst, MA 01003

Jason Stajich
jason at bioperl.org