Nonsynonymous and Synonymous Sites in A Gene

[rdoan]

Is it possible to predict the total possible synonymous and non-synonymous sites in a gene sequence? I would like a script where I can import a multi fasta file for several different genes and get the total number of possible synonymous and non-synonymous sites per gene.

I am not trying to identify synonymous and non-synonymous SNPs since I am only looking at a single sequence for each gene.

Thanks

[Torst]

I guess you would need to ALIGN all the coding sequences of the genes (either using codon-guided alignment, or align in protein space and work backwards).

Then, go through each codon position, and if there is a codon for every gene present at that position, and they aren't all the same, then collect stats about the syn and non-syn ones?