GSR: Simulator - 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 4 years ago
Homepagehttp://home.uchicago.edu/~rhudson1/source/mksamples.html
Citations Hudson RR, Generating samples under a Wright-Fisher neutral model of genetic variation., Bioinformatics, 02-01-2002 [ Abstract, cited in PMC ]
GSR Certification

Accessibility
Documentation
Application
Support

Last evaluated11-15-2018 (701 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataHaploid DNA Sequence,
VariationsSingle Nucleotide Variation,
Simulation MethodStandard Coalescent,
Input
Data Type
File format
Output
Data TypeGenotype or Sequence, Individual Relationship,
Sequencing Reads
File FormatMS,
Sample TypeRandom or Independent,
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Exponential Growth or Decline, Bottleneck,
Gene FlowStepping Stone Models, Island Models, Admixed Population, User-defined Matrix,
Spatiality
Life Cycle
Mating SystemRandom Mating,
Fecundity
Natural Selection
Determinant
Models
RecombinationUniform, Gene Conversion Allowed,
Mutation ModelsInfinite-sites Model,
Events AllowedPopulation Merge and Split, Varying Demographic Features,
Other
InterfaceCommand-line,
Development
Tested PlatformsMac OS X, Linux and Unix, Solaris,
LanguageC or C++,
LicenseGNU Public License,
GSR CertificationDocumentation, Application,

The following 5 publications are selected examples of applications that used ms.

2018

Price N, Moyers BT, Lopez L, Lasky JR, Monroe JG, Mullen JL, Oakley CG, Lin J, Ågren J, Schrider DR, et al., Combining population genomics and fitness QTLs to identify the genetics of local adaptation in <i>Arabidopsis thaliana</i>., Proc Natl Acad Sci U S A, 05-08-2018 [Abstract]

Legras JL, Galeote V, Bigey F, Camarasa C, Marsit S, Nidelet T, Sanchez I, Couloux A, Guy J, Franco-Duarte R, et al., Adaptation of S. cerevisiae to Fermented Food Environments Reveals Remarkable Genome Plasticity and the Footprints of Domestication., Mol Biol Evol, 07-01-2018 [Abstract]

Wang GD, Zhang BL, Zhou WW, Li YX, Jin JQ, Shao Y, Yang HC, Liu YH, Yan F, Chen HM, et al., Selection and environmental adaptation along a path to speciation in the Tibetan frog <i>Nanorana parkeri</i>., Proc Natl Acad Sci U S A, 05-29-2018 [Abstract]

Zhang C, Ni P, Ahmad HI, Gemingguli M, Baizilaitibei A, Gulibaheti D, Fang Y, Wang H, Asif AR, Xiao C, et al., Detecting the Population Structure and Scanning for Signatures of Selection in Horses (<i>Equus caballus</i>) From Whole-Genome Sequencing Data., Evol Bioinform Online, 06-04-2018 [Abstract]

Fujito NT, Satta Y, Hane M, Matsui A, Yashima K, Kitajima K, Sato C, Takahata N, Hayakawa T, Positive selection on schizophrenia-associated ST8SIA2 gene in post-glacial Asia., PLoS One, 07-25-2018 [Abstract]


Propose changes to this simulator