Hello there

I am a noob to WGS.

I am studying bacteria

The bug I am studying is quite variable

I sequenced some strains, assembled with SPADES and annotated with PROKKA.

I want to make snp calling based on the *.faa file. I want to use the amino acids and not the nucleic acid simply because the bacteria is very unstable genetically speaking and a snp call based on nucleic acid will probably return way too much snp that probably wont mean anything in tern of phylogeny.

I am trying to find tools and workflow that would allow that.

many thanks.