ms ( A program for generating samples under neutral models. )

Here is a LINK to source code and documentation for the program "ms" and "msHOT". ms is described in:

Hudson, R. R. (2002) Generating samples under a Wright-Fisher neutral model. Bioinformatics 18:337-8,

which is the proper citation for "ms". Full documentation is in the file msdoc.pdf. This pdf
file and all source code for ms are in the archive, ms.tar at the above link.
Download this tar file and type "tar xvf ms.tar", then type "cd msdir", then type "./clms" and you should be
ready to go. Type "./ms" for usage.

Note this is a new version (released Oct 14, 2007). This version fixes some problems that were occurring
with ms in Windows. Also the ms.tar file contains several examples of calling ms from R to
carry out Bayesian analyses.

Garrett Hellenthal and Matthew Stephens have produced a version of ms that allows hotspots of
recombination and gene conversion. The program, msHOT, is described in:

Hellenthal, G and M. Stephens. msHOT: modifying Hudson's ms simulator to incorporate crossover and
gene conversion hotspots. Bioinformatics. 2007 Feb 15;23(4):520-1.

Instructions and source code for msHOT can be found at the same link given above.