Basic Package AttributesAttribute | Value |
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Title | ForwSim |
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Short Description | The program given below is based on the algorithm described in Padhukasahasram et al. 2008 to simulate genetic drift in a standard Wright-Fisher process. |
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Long Description | Diploid organisms are represented as pairs of chromosome arrays that store the locations of mutations. The user specifies a probability of selfing. Populations of constant size reproduce with non-overlapping generations. Mutations occur at a Poisson-distributed rate and insert new integers into chromosome arrays, which may undergo recombination. The number of sites is finite, but mutations occur only at non-polymorphic sites. Locations which are no longer polymorphic are removed. If using natural selection, the evolution of selected and neutral sites is carried out separately, with selected sites considered first. |
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Project Started | 2009 |
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Last Release | 9 years, 1 month ago |
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Homepage | http://badri-populationgeneticsimulators.blogspot.com/ |
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Citations |
Padhukasahasram B, Marjoram P, Wall JD, Bustamante CD, Nordborg M, Exploring population genetic models with recombination using efficient forward-time simulations., Genetics, April 1, 2008
[Abstract, cited in
PMC
]
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GSR Certification |
This simulator has not yet been evaluated for GSR Certification. Learn more about or request GSR Certification.
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Recently certified
Author verification | The basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator. |
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Detailed AttributesAttribute Category | Attribute | Target | |
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Type of Simulated Data | Diploid DNA Sequence,
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Variations | Biallelic Marker,
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Simulation Method | Forward-time,
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Input | |
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Data Type | |
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File format | Program Specific,
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Output | |
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Data Type | Genotype or Sequence,
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Sequencing Reads | |
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File Format | Program Specific,
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Sample Type | |
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Phenotype | |
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Trait Type | |
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Determinants | |
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Evolutionary Features | |
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Demographic | |
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Population Size Changes | Constant Size,
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Gene Flow | |
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Spatiality | |
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Life Cycle | Discrete Generation Model,
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Mating System | Random Mating,
Selfing,
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Fecundity | |
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Natural Selection | |
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Determinant | Multi-locus,
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Models | Directional Selection,
Balancing Selection,
Multi-locus models,
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Recombination | Uniform,
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Mutation Models | Two-allele Mutation Model,
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Events Allowed | |
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Other | |
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Interface | Command-line,
Script-based,
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Development | |
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Tested Platforms | Windows,
Mac OS X,
Linux and Unix,
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Language | C or C++,
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License | GNU Public License,
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GSR Certification | |
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No example publication using ForwSim has been provided.
Please
propose new citations if you are aware of publications that use this software.