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GSR: Simulator - ForwSim
The ForwSim package is not yet public.
| Attribute | Value |
|---|---|
| Title | ForwSim |
| 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. |
| 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. |
| Project Started | 2009 |
| Last Release | 14 years, 3 months ago |
| Homepage | http://badri-populationgeneticsimulators.blogspot.com/ |
| Citations | Padhukasahasram B, Marjoram P, Wall JD, Bustamante CD, Nordborg M, Exploring population genetic models with recombination using efficient forward-time simulations., Genetics, 04-01-2008 [ Abstract, cited in PMC ] |
| GSR Certification | This simulator has not yet been evaluated for GSR Certification. Learn more about or request GSR Certification. |
| 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. |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Diploid DNA Sequence, |
| Variations | Biallelic Marker, |
| Simulation Method | Forward-time, |
| Input | |
| Data Type | |
| File format | Program Specific, |
| Output | |
| Data Type | Genotype or Sequence, |
| Sequencing Reads | |
| File Format | Program Specific, |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, |
| Gene Flow | |
| Spatiality | |
| Life Cycle | Discrete Generation Model, |
| Mating System | Random Mating, Selfing, |
| Fecundity | |
| Natural Selection | |
| Determinant | Multi-locus, |
| Models | Directional Selection, Balancing Selection, Multi-locus models, |
| Recombination | Uniform, |
| Mutation Models | Two-allele Mutation Model, |
| Events Allowed | |
| Other | |
| Interface | Command-line, Script-based, |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, |
| Language | C or C++, |
| License | GNU Public License, |
| GSR Certification |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using ForwSim has been provided.
Please propose new citations if you are aware of publications that use this software.