use codeml from PAML package. You can check if the resulting positive selected sites (from codeml) fall within a domain or on an active site. I use python to plot the observed pos sites on uniprot annotations. Codeml models are bit difficult to understand initially but worth taking a look at the manual and if you are aligning distant related species then be aware of the alignment errors. A lot of literature already available on this. Hope this helps.