phydms

phydms enables phylogenetic analyses using deep mutational scanning data to inform the substitution models. It implements Experimentally informed codon models (ExpCM) for phylogenetic inference and the detection of biologically interesting selection.

phydms is written by the Bloom lab (see https://github.com/jbloomlab/phydms/contributors for a full list of contributors).

See the phydms documentation for information about using phydms and details about the recommended installation process.

The phydms source code is freely available under a GPLv3 license.

If you use phydms, please cite it appropriately.