Question: How to get the number of segregating sites from a multiple alignment?
gravatar for Flávia Rogério
11 days ago by
São Paulo, Brazil
Flávia Rogério0 wrote:

Hi everyone!

I'm struggling to get the number of segregating sites (S) in a large contig in a fasta format (1.3Mb) with multiple sequences. I've used muscle aligner to get this alignment, and now I need the number, and % of segregating sites across all sequences from my contig. I didn't find info if muscle can provide it.

Any tips? Thanks!

ADD COMMENTlink modified 10 days ago by RamRS30k • written 11 days ago by Flávia Rogério0
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