Hi Michael,

this is possible with PAML. You have to choose between different models: branch-specific model, site-specific model or branch-site model. They are all detailed in the PAML documentation. You can also check this online course for a more user friendly help. The PAML FAQ can also be of interest for some specific questions.

By the way, the common name for the ratio is either Ka/Ks or dN/dS, but not Kn/Ks.

Hi, I am not sure you can find something about selective pressure by site doing pure pairwise analysis (runmode = -2), this is usually used for global distances. On the other hand doing site analysis you can get this info by site, but it is generally a bad idea to use this result when analyzing less than 4 sequences (if you try it, have a look to associated errors of the estimations).

have a look to this post: http://gsf.gc.ucdavis.edu/viewtopic.php?f=1&t=1099

an other program that can do this for you is SLR http://www.ebi.ac.uk/goldman/SLR/ but I am afraid that you will find same restrictions...

I think the best solution, if you can, is to group your sequences by 4.