Substitution Matrix For Multiple Alignment File

Question

[Smack The insect]

Hi all,

this will be my first question here :)

i have an alignement file generated using Clustalx (around 20 species)

i need to parse this file using biopython in order to get for each position in the alignement the substitution matrix.

is this can be done??? and how??

thank you.

Answer 1

[Peter]

You can load a multiple sequence alignment in Biopython like so:

from Bio import AlignIO
align = AlignIO.read("my_file.aln", "clustal")

Then you might loop over each column.

I would like to be able to direct you to a pertinent example in the Tutorial http://biopython.org/DIST/docs/tutorial/Tutorial.html but I've just noticed the substitution matrix from an alignment example which would be close, is out of date (the old Bio.Clustalw module was deprecated and removed). I have filed a bug https://redmine.open-bio.org/issues/3340

[Smack The insect]

Hi, thank you for your answer, i already now how to do this, but i'm new to python and biopython, and i don't know to deal with such things, can you point me on how to do this?? or is it possible to get the substitution matrix using another sofrware and then use it in the script?? (PHYML oe Mr.Bayes)