I have performed an amino acid alignment on MEGA, however I am interested in knowing the proportions of different amino acids found on each polymorphic site. It does not seem that MEGA would perform that.
Worst worst case I can use excel and use "advanced filter" to tabulate the number of different amino acids on each substitution site, however it's an alignment of 350+ sequences to look at and I have almost 100 substitution sites to analyze.
I was wondering if there is a freeware out there which can perform the following:
1) translate a nucleotide alignment to protein sequence alignment
2) calculate the proportions of different amino acids for each substitution site (e.g. tyr in 30/365 of sequences, ala in 335/365 of sequences, etc)
Thank you so much
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Help with Amino Acid alignment software
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