Software to produce position-specific conservation of multiple sequence alignment results?

Question

[O.rka]

I have a bunch of multiple sequence alignment files in fasta format. They have gap characters as "-" and they are in protein space. I'd like to get a table that has a score for each position. I can code one myself but feel that I would be reinventing the wheel. I could do a naive one but I'm sure having an alignment blosum matrix would be the best way forward which I would likely mess up.

Is there a software where I could do the following or similar (either commandline or Python):

cat alignment.fasta.msa | [some program] > position_specific_conservation.tsv

Answer 1

[Mensur Dlakic]

There are servers and programs that will calculate what you want, though it may not be in the format you desire.

• http://prodata.swmed.edu/al2co/al2co.php
• https://compbio.cs.princeton.edu/conservation/