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.
For each alignment, FitMulti model fits five models, all extenstions of the Muse and Gaut (1994) codon model allowing for multiple instantaneous nucleotide changes within a codon to occur. Then pairwise likelihood ratio tests are performed between the models. This requires a codon alignment and a tree.
- Output includes the rate estimates for each model, the LRT p values, and a list of sites that show strong preference for multiple hit models.
- Can be used to determine the extent of multiple hits present in a data set.