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msBayes

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.

BUGS

Please update to version 20080613, version 20080515 was not functional.

Download

Current version: 20080613

Source code (tar ball)

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