I've received an e-mail from a user asking about how to replicate a pairwise test of differences in dN/dS between particular taxa following a Nei-Gojobori counting method for positive selection in HyPhy.

Currently, we don't have a batch file for doing this, although it is possible to modify the existing implementation of the counting method (SLAC) to do so.  There are several statistical reasons (e.g. multiple comparisons) not to use this sort of pairwise analysis in the first place.  I'm starting a thread on this topic for further discussion.

- Art.