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 Jesse Bloom, and uses the Bio++ libraries for likelihood calculations (thanks to Julien Dutheil and Laurent Gueguen for making these wonderful libraries available).
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 (the Bio++ and LSD source code is packaged into the phydms source code; these code bases are themselves under a GPL-compatible CeCILL license and a GPLv3 license, respectively).