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GSR: Simulator - forqs
| Attribute | Value |
|---|---|
| Title | forqs |
| Short Description | Forward-in-time simulation of Recombination, Quantitative Traits, and Selection |
| Long Description | forqs is a forward-in-time population genetics simulation that tracks individual haplotype chunks as they recombine each generation. forqs also also models quantitative traits and selection on those traits. forqs is implemented as a command-line C++ program, using a modular design that gives the user great flexibility in creating custom simulations. It is freely available with a permissive BSD license. |
| Version | by date |
| Project Started | 2013 |
| Last Release | 11 years, 7 months ago |
| Homepage | https://bitbucket.org/dkessner/forqs |
| Citations | Kessner D, Novembre J, forqs: forward-in-time simulation of recombination, quantitative traits and selection., Bioinformatics, Feb. 15, 2014 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | Sept. 8, 2017 (2927 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Diploid DNA Sequence, Haploid DNA Sequence, |
| Variations | Biallelic Marker, Multiallelic Marker, Single Nucleotide Variation, |
| Simulation Method | Forward-time, |
| Input | |
| Data Type | |
| File format | Program Specific, |
| Output | |
| Data Type | Genotype or Sequence, Phenotypic Trait, Mutation, Linkage Disequilibrium, Fitness, |
| Sequencing Reads | |
| File Format | Program Specific, |
| Sample Type | |
| Phenotype | |
| Trait Type | Binary or Qualitative, Quantitative, Multiple, |
| Determinants | Single Genetic Marker, Multiple Genetic Markers, Sex-linked, Environmental Factors, |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Exponential Growth or Decline, Logistic Growth, Bottleneck, User Defined, |
| Gene Flow | Stepping Stone Models, Island Models, Continent-Island Models, Admixed Population, Other, |
| Spatiality | |
| Life Cycle | Discrete Generation Model, |
| Mating System | Random Mating, Other, |
| Fecundity | Randomly Distributed, |
| Natural Selection | |
| Determinant | Single-locus, Multi-locus, Fitness of Offspring, Phenotypic Trait, Environmental Factors, |
| Models | Directional Selection, Balancing Selection, Multi-locus models, Epistasis, Phenotype Threshold, |
| Recombination | Uniform, Varying Recombination Rates, |
| Mutation Models | Two-allele Mutation Model, k-Allele Model, |
| Events Allowed | Population Merge and Split, Varying Demographic Features, Population Events, |
| Other | Polygenic background, |
| Interface | Command-line, |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, |
| Language | C or C++, |
| License | BSD, |
| GSR Certification | Accessibility, Documentation, Application, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used forqs.
2023
Drury AL, Gout JF, Dapper AL, Modeling Recombination Rate as a Quantitative Trait Reveals New Insight into Selection in Humans., Genome Biol Evol, Aug. 1, 2023 [Abstract]
2021
Frayer ME, Payseur BA, Demographic history shapes genomic ancestry in hybrid zones., Ecol Evol, July 5, 2021 [Abstract]