Hi all again,
I've noticed that most programs used to predict the effect of non-synonymous amino acids substitutions simply don't analyze the action of selection of any kind. Given that conservation in alignment does not mean necessarily purifying selection, I'm wondering about the true relation between conservation and selection. In order to test this idea, I really need some guidelines to calculate Ka/Ks in close and distantly related species. Any software able to deal with such situation is much welcome too!
-- Edit --
I know a lot of programs able to calculate Ka/Ks. What I really want is an expert opinion of what to do and which one to use.