Does EMBOSS have an associated program that will calculate dN, dS (non-synonymous/synonymous substitutions) for a multiple sequence alignment?
If so, what is the program, and can it use a tree file to determine the actual number of substitutions rather than just tallying the raw number based on pairwise comparisons?
I looked at the program list here and didn't see anything specific, but perhaps I missed something or it's documented in a way that I misread:
http://emboss.sourceforge.net/apps/cvs/emboss/apps/index.html