This work is licensed under a Creative Commons Attribution 4.0 International License.
PyMsBayes provides a multi-processing interface to the comparative phylogeographic software packages dpp-msbayes and msBayes. More generally, PyMsBayes can serve as a multi-processing Python API for inferring comparative models of diversification via approximate Bayesian computation (ABC). For more details about the methods implemented in PyMsBayes checkout the background section. You should also be aware of relevant caveats before using the method. The package is written by Jamie Oaks.
PyMsBayes is essentially a multi-processing wrapper around some popular ABC tools. Executables of the following tools come bundled with PyMsBayes:
- dpp-msbayes
- msBayes
- ABCtoolbox
- euReject of the ABACUS package
Executables for Linux and Mac are included. The Linux executables are statically linked and should run on any 32-bit or 64-bit Linux system. The Mac executables are universal (built for architectures ppc, i386, and x86_64) and mostly statically-linked, and so should work on any Mac. But, Macs are weird, so no promises. See the “Installation” section for more details about installing the bundled tools.
This software greatly benefited from funding provided to Jamie Oaks from the National Science Foundation (DEB 1011423 and DBI 1308885), University of Kansas (KU) Office of Graduate Studies, Society of Systematic Biologists, Sigma Xi Scientific Research Society, KU Ecology and Evolutionary Biology Department, and the KU Biodiversity Institute.
Some of the functions for calculating properties of Dirichlet processes were adapted from functions within util.h from the software package DPPDiv version 1.0b (Copyright Tracy Heath, Mark Holder, and John Huelsenback; licensed under GPL v3; http://phylo.bio.ku.edu/content/tracy-heath-dppdiv).
If you have questions regarding the installation or use of PyMsBayes, or you just want to stay informed about version releases and other news about the package, join the PyMsBayes user’s group at https://groups.google.com/forum/?hl=en#!forum/pymsbayes-users.