| Long Description || This document describes how to use msms, a tool to generate sequence samples under both neutral models and a single locus selection model. msms permits the full range of demographic models provided by ms(Hudson, 2002). In partic-ular, it allows for multiple demes with arbitrary migration patterns, population growth and decay in each deme, and for population splits and mergers. Selection (including dominance) can depend on the deme and also change with time. The program is designed to be command line compatible to ms, however no prior knowledge of ms is assumed for this document. Applications of this program include power studies, analytical comparisons, approximated Bayesian computation among many others. Because most applications require the generation of a large number of independent replicates, the code is designed to be efficient and fast. For the neutral case, it is comparable to ms and even faster for large recombination rates. For selection, the performance is only slightly slower, making this one of the fastest tools for simulation with selection.
The program has been developed with a wide number of possible operating systems and hardware in mind. For this reason, the code has been developed in Java and can run on any hardware that supports Java 1.6. This includes Mac OS X, all current versions of MS Windows, and most Unix flavors (Linux, Sun, BSD). The Java programing language is also popular and widely known which should facilitate the writing of extensions for the program. |
Ewing G, Hermisson J, MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus., Bioinformatics, Aug. 15, 2010
[Abstract, cited in