[Biopython] User Defined Scoring Matrix

[Peter Cock]

On Fri, Feb 22, 2013 at 2:19 AM, Willis, Jordan R
<jordan.r.willis at vanderbilt.edu> wrote:
> Hello,
>
> Since I'm not sure which tool to exactly use, I will defer to the
> biopython community since odds are I will be using it. I'm trying to produce
> a multiple sequence alignment with a user defined scoring matrix. When I
> look at Clustalw, there is an option to put in such a matrix, and the help
> indicates that this should be in "blast" format. When I search for blast
> format, they indicate that this is hard coded into the software.

I wouldn't start with ClustalW - it is old and still widley used, but even
the authors are trying to discourage this. They suggest their new tool
Clustal Omega, and that as a Biopython wrapper and takes an optional
distance matrix as input via the --distmat-i argument.

from Bio.Align.Applications import ClustalOmegaCommandline
help(ClustalOmegaCommandline)

http://biopython.org/DIST/docs/api/Bio.Align.Applications._ClustalOmega.ClustalOmegaCommandline-class.html

> My end goal is to produce a phylogeny tree using this PSSM, but I have no
> idea how to input this into ClustalW or any multiple sequence alignment
> software. I don't really care which software to use, which wrappers, or how
> I have to do it.I have used biopython to produce this matrix, so I thought
> it would be relatively easy to implement it in any multiple sequence
> alignment software.
>
> I'm not having very good luck and any help would be must appreciated.
>
> Jordan

There are people far more qualified than me to comment on the
goals and if and when you should use a distance based tree (my
understanding is distance based trees are the worst kind, but as
they are computationally inexpensive make can sense for large
datasets).

Regards,

Peter