[Biopython] Mafft Alignment Output file

[Peter]

On Mon, Nov 29, 2010 at 10:26 AM, Ömer <arkanion at gmail.com> wrote:
> I installed mafft.bat file to run an alignment similar to clustalw.exe
> shown in the Tutorial. I prefer Mafft because it has an  option to
> choose the matrix such as Blosum 45 , 80 etc.

I think MAFFT is also faster, especially with large alignments.

> 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?
> It has parameters for the output file but the file cannot be created itself
> ! It is simply generated by default when used ClustalWCommandline.
> I checked everywhere but couldn't find ! Any idea?

What are you doing right now? Can you show us your code?

Are you using the MafftCommandline wrapper as I suggested here?:
http://lists.open-bio.org/pipermail/biopython/2010-November/006894.html

I'm looking at the code right now, and it could do with a basic example.

Peter