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
Binary
- RPMs
These binaries are statically linked, so it should work in most
distributions without installing GSL. But you do need to install
other components described in Installation
instructions
- Mac OS-X (ppc, intel)
It
was compiled on Mac OS-X 10.5. I'm not sure if it runs on other
version of OS-X. GSL is statically linked, so you do not need to
install it. The examples and documents are not included, but you can
get them from the source distribution.
If you want to install it in your home directory, do the following in
Terminal.app (I'm assuming that you downloaded the binary to your
desktop).
cd; tar xzvf Desktop/msbayes-mac-xxxxxxxx.tgz -C ~
Substitute xxxxxxxx with the appropriate version number.
