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GSR: Simulator - GenomePop2
| Attribute | Value |
|---|---|
| Title | GenomePop2 |
| Short Description | GenomePop2 is a specialization of the program GenomePop just to manage SNPs under more flexible and useful settings. If you need models with more than 2 alleles please use the GenomePop program version. |
| Long Description | This new version allows the forward simulation of sequences of biallelic positions. As in the previous version, a number of evolutionary and demographic settings are allowed. Several populations under any migration model can be implemented, contraction-expansion scenarios, directional or divergent selection. Theoretical or simulated initial equilibrium population can be computed the same as speciation processes via the simulation of user-defined population splits. Each population consists of a number N of individuals. Each individual is represented by one or more chromosomes with constant or variable (hotspots) recombination between binary sites. |
| Version | 2.6.2 |
| Project Started | 2010 |
| Last Release | 10 years, 6 months ago |
| Homepage | http://acraaj.webs.uvigo.es/GenomePop2.htm |
| Citations | Carvajal-Rodríguez A, GENOMEPOP: a program to simulate genomes in populations., BMC Bioinformatics, April 30, 2008 [ Abstract, cited in PMC ] |
| GSR Certification | Accessibility |
| Last evaluated | May 17, 2018 (2677 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Genotype at Genetic Markers, Mitochondrial DNA (Version 2.8 or later), |
| Variations | Biallelic Marker, Multiallelic Marker (The user only needs to define a given region without recombination (linked) and with a non-zero mutation rate ), |
| Simulation Method | Forward-time, |
| Input | |
| Data Type | Allele Frequencies (See howto 14 from the web page), |
| File format | Other (Fasta version 2.6 or later), |
| Output | |
| Data Type | Genotype or Sequence, |
| Sequencing Reads | |
| File Format | Genepop, MS, Phylip, |
| Sample Type | Random or Independent (The user can define the population size and the sample size. ), |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Bottleneck, Carrying Capacity, User Defined, |
| Gene Flow | Stepping Stone Models, Island Models, Continent-Island Models, User-defined Matrix, |
| Spatiality | |
| Life Cycle | Discrete Generation Model, |
| Mating System | Random Mating, Polygamous (Depending on fitness as defined by the genotype), Selfing, |
| Fecundity | Constant Number, Individually Determined (Depending on fitness as defined by the genotype. ), |
| Natural Selection | |
| Determinant | Single-locus (User-defined), Multi-locus (User-defined), |
| Models | Directional Selection, Balancing Selection (User-defined via negative dominance coefficient), Multi-locus models, Random Fitness Effects, |
| Recombination | Uniform, Varying Recombination Rates, |
| Mutation Models | Two-allele Mutation Model, Infinite-sites Model, |
| Events Allowed | Population Merge and Split, |
| Other | |
| Interface | Command-line, Graphical User Interface (Version 2.7 or later), |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, |
| Language | C or C++, Java (For gui and from version 2.7 or later), |
| License | GNU Public License, |
| GSR Certification | Documentation, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using GenomePop2 has been provided.
Please propose new citations if you are aware of publications that use this software.