For each site in a codon alignment, estimate whether or not dN/dS ratios differ between sets of branches defined a priori. If the branches are associated with different selective environments, this could be used to generate a list of sites that may be evolving at different rates (under different selective pressures) in these environments.
- Outputs a list of sites where
testbranches have a statistically detectable difference in dN/dS from
- Could be used to test for differential selection pressures, for example between host and recipient or individual anatomical compartments in HIV-1, or in between species with different phenotypes/traits.