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msBayes (pronounced em es bayeszzz) allows complex and flexible comparative phylogeographic inference.

More specifically, you can test for simultaneous divergence or colonization across multiple co-distributed pairs of taxa (populations and/or species). It uses hierarchical approximate Bayesian computation (HABC) to estimate hyper-parameters given DNA sequence data. The HABC algorithm uses a finite sites version of ms, the classic coalescent simulator written by Dick Hudson.

The hierarchical model incorporates uncertainty into each set of the taxon-pair demographic parameters (sub-parameters) while estimating hyper-parameters that characterize the congruence in divergence/colonization times across the co-distributed taxon-pairs.

This program is developed by Mike Hickerson, Eli Stahl, Wen Huang, and Naoki Takebayashi and released under the GNU Public License.

msBayes runs on Linux, Mac OS-X, and most POSIX systems. Although you need to use command line interface, it is fairly simple. Installation instructions and user documentation are available. Here are additional tips for users who can't install the required programs due to the lack of the root (super-user) access to the computer. Also check out additional tips, scripts from Mike's homepage.


March 5, 2014, Fixed compatibility with the newer VGAM R package. Mac binary should run in any version of Mac OS-X now. No need to upgrade to this version if your current version is working.

June 11, 2013, Fixed a small bug, which get triggered when a locus without polymorphism is included.

May 10, 2012, A small, but annoying bug is fixed. There was very rare instances where stalls out without completing all simulations. This is fixed now, and we highly recommend the update with this version. Feb. 22, 2012, Release of new version with bug fix.

May 19, 2010, Multi-locus version of msBayes (MTML-msBayes) released!

Earlier versions may contain bugs, so please update to this newest version.


Current version: 20140305

Source code (tar ball)


Older version

Last single locus version: 20081106

This is the older version which uses single locus data sets. Multi-locus version (version 20100519 and newer) can do single-locus analyses and it has additional capabilities. So please use the newer version. The format of configuration file has been slightly changed, but it should be easy to convert the older batch config file to the newer format.

Source code (tar ball)