ms

Basic Package Attributes
AttributeValue
Title ms
Short Description The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets.
Long Description The program ms can be used to generate many independent replicate samples under a variety of assumptions about migration, recombination rate and population size to aid in the interpretation of such polymorphism studies. The samples are generated using the now standard coalescent approach in which the random genealogy of the sample is rst generated and then mutations are randomly place on the genealogy (Kingman, 1982; Hudson, 1990; Nordborg, 2001). The usual small sample approximations of the coalescent are used. An infinitesites model of mutation is assumed, and thus multiple-hits and back mutations do not occur. However, when used in conjunction with other programs, finite-site mutation models or micro-satellite models can be studied. For example, the gene trees themselves can be output, and these gene trees can be used as input to other programs which will evolve the sequences under a variety of finite-site models. These are described later. The program is intended to run on Unix, or Unix-like operating systems, such as Linux or MacOsX. The next section describes how to download and compile the program. The subsequent sections described how to run the program and in particular how to specify the parameter values for the simulations.
Version 20161016
Project Started 2002
Last Release 2 years, 1 month ago
Homepagehttp://home.uchicago.edu/~rhudson1/source/mksamples.html
Citations Hudson RR, Generating samples under a Wright-Fisher neutral model of genetic variation., Bioinformatics, Feb. 1, 2002 [Abstract, cited in PMC ]
GSR CertificationAccessibility
Documentation
Application
Support
Propose changes to this simulator