[Biopython-dev] [Biopython] Biopython library for muliple sequence alignment

[Peter Cock]

On Wed, Feb 23, 2011 at 6:42 AM, Rojan Shrestha <rojan at riken.jp> wrote:
> Hello:
>
> I want to do multiple sequence alignment using CLUSTW. Instead of
> standalone, I would like to use in my own program through biopython. I would
> like to know that whether biopython has clustw function or not. It would be
> very good if somebody  gives information about this.
>
> Regards,
>
> Rojan

Hello Rojan,

Biopython (and BioPerl too I believe) doesn't have any multiple sequence
alignment code itself. Biopython does has pairwise sequence alignment
code (with a fast implementation in C).

Instead (again, like BioPerl) Biopython has a wrapper and parser for
calling the ClustalW command line tool from within your script and
loading its output. Similarly for other alignment tools like Muscle.

If you really want to be able modify the multiple sequence alignment
code itself, some of these command line tools are open source. Also,
I *think* that BioJava has some code for this.

I don't know what BioRuby does.

Peter

P.S. You only really need to ask this on the Biopython Discussion List.
Since you included the OBF cross project list I have tried to comment
on how the other projects handle this as well.