I have a list of the numbers of synonymous and non-synonymous SNPs for a large set of genes (please note - do not have the actual SNP sequences just the amounts).
I would like to now calculate the ka/ks ratio however to do so I need to calculate the numbers of synonymous and non synonymous sites in each gene. I can find a lot of information on how to calculate the ka/ks ratio but not for how to get how many sites have the potential to host either synonymous or non-synonymous substitutions.
Any advice how to do so? Especially bearing in mind I am not great at programming - I can run R but do not have access at the moment to things like matlab.
Thanks in advance for any feedback - am a first time user so happy to give more info. Daisy