Documentation for phydms

phydms is a software package for phylogenetic analyses using deep mutational scanning data to inform the substitution models.

phydms can use Experimentally Informed Codon Models to describe the evolution of protein-coding genes for phylogenetic analyses and the detection of sites of biologically interesting selection.

phydms is written in Python by Bloom lab (see the full list of contributors).

Installation of phydms will install the phydms program, which performs the phylogenetic analyses. It also installs auxiliary programs that facilitate model comparisons and visualization of the results. All of these programs are installed as command-line executables.

See how to use phydms for more details and a tutorial on how to use phydms.

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

If you use phydms, please cite the references in Acknowledgments and citations.

Contents

• Installation
• how to use phydms
• the phydms program
• auxiliary programs
• Experimentally Informed Codon Models
• Numerical implementation
• phydmslib package
• Acknowledgments and citations
• Indices and tables