[Bioperl-l] MSA manipulation

Jason Stajich jason at bioperl.org
Tue May 13 13:25:42 EDT 2008


Jon -

[CC-ing list in case others have input.]

AlignI is the interface module but the actual implementation is in  
Bio:SimpleAlign.

You want to read in alignments with Bio::AlignIO and that will give  
you Bio::SimpleAlign objects that can then be manipulated.
There are methods for removing columns, etc.

-jason
On May 13, 2008, at 2:35 AM, Jon Wright ((JIC)) wrote:

> Hi Jason,
>
>
>
> I am looking for a bioperl module into which you can load a multiple
> sequence alignment and manipulate it programmatically (similar to
> something like Jalview).  The closest thing in BioPerl that I can find
> is your implementation of the Bio::Align::AlignI but this doesn't  
> allow
> any manipulation as far as I can tell.  Are you aware of anything else
> that might do the job?
>
>
>
> Thanks for your help.
>
>
>
> Jon
>
>
>
> *********************************************************
>
> Jonathan Wright
>
> Computational and Systems Biology Department
>
> John Innes Centre
>
> Norwich
>
> UK
>
>
>
> www.jic.bbsrc.ac.uk
>
> Tel. +44 (0)1603 450811
>
> *********************************************************
>
>
>



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