How to calculate dN/dS for all ortholog group ?

Question

[sadstudent]

Hi all,

I have managed to generate json file for all ortholog groups (4000) under HyPhy using BUSTED, SLAC and FEL. From the output, how can i find the dN/dS and how shall i compare among all of the groups ? In addition, what other information can i retrieve from this output ? Do enlighten me in this issue.

Thank you.

[lagartija]

I use codeml on neutral model but it is really non trivial