Analysis list#

This is not a complete list, but the new analyses will be described here. Other places to look are manuscript associated analyses, and the GitHub boards


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 test branches have a statistically detectable difference in dN/dS from reference branches.
  • 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.

Further information


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.

Further information