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GSR: Simulator - invertFREGENE
| Attribute | Value |
|---|---|
| Title | invertFREGENE |
| Short Description | InvertFREGENE is a forward-in-time simulator of inversions in population genetic data |
| Long Description | invertFREGENE is the forward-in-time simulator of inversions in population genetic data, while SAMPLE samples genotype and haplotype data from the output of invertFREGENE simulations based on specified individual and marker ascertainment criteria, including a continuous and case-control disease model. invertFREGENE has been developed from a beta version of the population genetic simulator FREGENE, and as a result there are a small number of features not included in invertFREGENE (eg. it does not model natural selection), therefore we provide self-contained documentation for invertFREGENE. O'Reilly PF, Coin LJ, Hoggart CJ. invertFREGENE: software for simulating inversions in population genetic data. Bioinformatics. 2010 Mar 15;26(6):838-40. |
| Project Started | 2009 |
| Last Release | 15 years, 11 months ago |
| Homepage | http://www.ebi.ac.uk/projects/BARGEN/ |
| Citations | O'Reilly PF, Coin LJ, Hoggart CJ, invertFREGENE: software for simulating inversions in population genetic data., Bioinformatics, March 15, 2010 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | May 2, 2019 (2327 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Diploid DNA Sequence, Haploid DNA Sequence, |
| Variations | Biallelic Marker, Single Nucleotide Variation, Inversion and Rearrangement (Inversion), |
| Simulation Method | Forward-time, |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | Genotype or Sequence, Phenotypic Trait (Using sample), Demographic, Diversity Measures, |
| Sequencing Reads | |
| File Format | Program Specific, |
| Sample Type | Random or Independent, Case-control (Using sample), |
| Phenotype | |
| Trait Type | Quantitative (Using sample), |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Bottleneck (Using consecutive invertfregene simulations), User Defined (Using consecutive invertfregene simulations), |
| Gene Flow | Island Models, User-defined Matrix, |
| Spatiality | |
| Life Cycle | |
| Mating System | Random Mating, |
| Fecundity | |
| Natural Selection | |
| Determinant | Single-locus, Multi-locus, |
| Models | Multi-locus models, |
| Recombination | Uniform, Varying Recombination Rates, Gene Conversion Allowed, |
| Mutation Models | Two-allele Mutation Model, |
| Events Allowed | |
| Other | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | 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 invertFREGENE has been provided.
Please propose new citations if you are aware of publications that use this software.