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GSR: Simulator - SNPsim
| Attribute | Value |
|---|---|
| Title | SNPsim |
| Short Description | Coalescent simulation of hotspot recombination |
| Long Description | SNPsim is a population genetic simulator that generates samples of SNP (Single Nucleotide Polymorphisms) haplotypes and diploid biallelic genotypes. It is based on the coalescent with recombination (Hudson 1983) modified by Wiuf and Posada (2003) to include recombination hotspots. SNPsim also allows for the specification of demographic periods and different mutation models. |
| Version | 0.8 |
| Project Started | 2003 |
| Last Release | 19 years, 11 months ago |
| Homepage | http://code.google.com/p/phylosoftware/ |
| Citations | Posada D, Wiuf C, Simulating haplotype blocks in the human genome., Bioinformatics, 01-22-2003 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | 10-15-2020 (1276 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Genotype at Genetic Markers, Diploid DNA Sequence, Haploid DNA Sequence, |
| Variations | Biallelic Marker, |
| Simulation Method | Standard Coalescent, |
| Input | |
| Data Type | |
| File format | Program Specific, |
| Output | |
| Data Type | Genotype or Sequence, Individual Relationship, |
| Sequencing Reads | |
| File Format | Program Specific, |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Exponential Growth or Decline, User Defined, |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | Random Mating, |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | Varying Recombination Rates, |
| Mutation Models | Two-allele Mutation Model, Infinite-sites 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 | Accessibility, Documentation, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using SNPsim has been provided.
Please propose new citations if you are aware of publications that use this software.