Synonymous and asynonymous sites in Ka/Ks
Ka/Ks ration is the number of nonsynonymous substitutions per nonsynonymous site (Ka) to the number of synonymous substitutions per synonymous site (Ks). I am struggling to find what is "total number of synonymous sites (or nonsynonymous sites)" between two sequences. Not very much interested on how they are calculated but what is this?
Does PAML (codeml) or any other program calculating Ka/Ks, determine "total number of synonymous sites (or nonsynonymous sites)" between two sequences, by multiple alignment of the given gene by looking into sequence beyond the two sequences given to come with the total number of synonymous (or nonsynonymous sites)?
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