[Biopython] Using ClustalW Webtool

[Peter]

On Mon, Nov 29, 2010 at 12:40 AM, Ömer AN <bounlu at gmail.com> wrote:
>
> One last vital question I have. I installed mafft.bat file to run an
> alignment similar to clustalw.exe. It is better for me because it has an
> option to choose the matrix such as Blosum 45 , 80 etc. However, it does not
> generate an output file by default for the alignment ! How can I create an
> output file? Which option should i switch on or what value should i assign?
> So that i can read the alignment file via AlignIO? I checked everywhere but
> couldn't find !
>

The Tutorial doesn't (currently) show any MAFFT examples, but you
would use the MafftCommandline wrapper class from the module
Bio.Align.Applications very similarly to how you use ClustalW with
ClustalwCommandline.

Peter

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the discussion, or help. Thanks!