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GSR: Simulator - ms
| Attribute | Value |
|---|---|
| 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 | 7 years, 6 months ago |
| Homepage | http://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 |
| Last evaluated | 11-15-2018 (1976 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Haploid DNA Sequence, |
| Variations | Single Nucleotide Variation, |
| Simulation Method | Standard Coalescent, |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | Genotype or Sequence, Individual Relationship, |
| Sequencing Reads | |
| File Format | MS, |
| Sample Type | Random or Independent, |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Exponential Growth or Decline, Bottleneck, |
| Gene Flow | Stepping Stone Models, Island Models, Admixed Population, User-defined Matrix, |
| Spatiality | |
| Life Cycle | |
| Mating System | Random Mating, |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | Uniform, Gene Conversion Allowed, |
| Mutation Models | Infinite-sites Model, |
| Events Allowed | Population Merge and Split, Varying Demographic Features, |
| Other | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | Mac OS X, Linux and Unix, Solaris, |
| Language | C or C++, |
| License | GNU Public License, |
| GSR Certification | Documentation, Application, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 5
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]