phyloExpCM documentation¶
This package is obsolete!¶
IMPORTANT NOTE: phyloExpCM has been superseded by phydms. Unless you need legacy functions of phyloExpCM, we recommend that you use phydms instead.
Package overview¶
phyloExpCM is a Python package for implementing experimentally determined codon models of substitution for phylogenetics.
Written by Jesse Bloom.
Source code is available on GitHub.
phyloExpCM documentation is available on GitHub pages.
Overview¶
This package contains scripts for performing codon-level analyses of phylogenetic trees. It is designed for a situation in which you would like to estimate a tree topology (for example with codonPhyML), and then use HYPHY to compare the extent to which various codon substitution models can describe the evolution of sequences within that tree topology. It is specifically designed to allow you to test experimentally determined codon models working with the output from the mapmuts package.
This package can be run using a series of scripts which are documented individually. You should be able to run analyses using this package by running those scripts without interfacing directly with the Python modules.