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I have an MSA from MAFFT (as a FASTA file; there are several sequences in the MSA), and I would like to quantify the "variants" between these sequences.

What is the standard tool to do something like this?

I would prefer to know the non-consensus variants in the the entire MSA, but that may be too tricky, so I would like to figure out the non-consensus variants between those select sequences.

I'm familiar with calculating an MSA, and then visualizing it---but I would like an output file with all of the different bases.

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    $\begingroup$ This is surprisingly not done or requested in the community, I'm also struggling. $\endgroup$ Oct 20 at 14:00
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A very basic solution in python:

from Bio import SeqIO
seq_dict = {i : rec.seq for i,rec in enumerate(SeqIO.parse("your_msa.aln", "fasta"))}
for pos in range(len(seq_dict[0])):
    pos_bases = ([seqio[i] for seqio in [*seq_dict.values()]])
    # If position contains more than one unique base
    if len([*set(pos_bases)])>1:
        print(pos, pos_bases)        # prints the position and alternative bases there

If you need something more useful, just leave a comment here and I'll develop this further.

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