EMBOSS program for calculating dN/dS from MSA

Question

[shpak.max]

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

Answer 1

[Mark]

Not sure about EMBOSS software suite, but I know PAML is standard for this operation. Here's a detailed protocol that outlines how to do this: https://www.protocols.io/view/introduction-to-calculating-dn-ds-ratios-with-code-qhwdt7e

Hope that helps

[shpak.max]

Thanks. The protocols.io site is temporarily down, so I have a quick question: when PAML computes dn/ds, does it take a tree file as input along with the MSA (and thus count the actual number of substitutions based on tree nodes), or does it do pairwise comparisons of all sequences regardless of phylogeny (treating each variant as statistically independent)?