How to get the number of segregating sites from a multiple alignment?

Question

[Flávia Rogério]

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!