## 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

### FEL-contrast#

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