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GSR: Simulator - FFPopSim
| Attribute | Value |
|---|---|
| Title | FFPopSim |
| Short Description | C++/Python library for population genetics. |
| Long Description | FFPopSim is a C++ and Python library to simulate large populations that are polymorphic at many loci. It allows for complex fitness functions, including pairwise and higher order epistasis. It is designed to study the effects of linked selection, the rare processes in large populations, and can be used to address a large variety of population genetics problems. |
| Version | 2.0 |
| Project Started | 2012 |
| Last Release | 11 years, 2 months ago |
| Homepage | http://webdav.tuebingen.mpg.de/ffpopsim/ |
| Citations | Zanini F, Neher RA, FFPopSim: an efficient forward simulation package for the evolution of large populations., Bioinformatics, 12-15-2012 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | 11-10-2017 (2346 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Haploid DNA Sequence, |
| Variations | Biallelic Marker, |
| Simulation Method | Forward-time, Phylogenetic, |
| Input | |
| Data Type | Allele Frequencies, Empirical, Ancestral Sequence, Saved simulation, |
| File format | Program Specific, |
| Output | |
| Data Type | Genotype or Sequence, Phenotypic Trait, Demographic, Linkage Disequilibrium, Diversity Measures, Fitness, |
| Sequencing Reads | Other, |
| File Format | Program Specific, |
| Sample Type | Longitudinal, |
| Phenotype | |
| Trait Type | Binary or Qualitative, Quantitative, Multiple, |
| Determinants | Single Genetic Marker, Multiple Genetic Markers, Gene-Gene Interaction, Environmental Factors, Gene-Environment Interaction, |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Exponential Growth or Decline, Logistic Growth, Bottleneck, Carrying Capacity, User Defined, |
| Gene Flow | |
| Spatiality | |
| Life Cycle | Discrete Generation Model, |
| Mating System | Random Mating, |
| Fecundity | Randomly Distributed, |
| Natural Selection | |
| Determinant | Single-locus, Multi-locus, Codon-based, Fitness of Offspring, Phenotypic Trait, Environmental Factors, |
| Models | Directional Selection, Balancing Selection, Multi-locus models, Epistasis, Random Fitness Effects, Disruptive, Phenotype Threshold, Frequency-Dependent, Other, |
| Recombination | Uniform, Varying Recombination Rates, |
| Mutation Models | Two-allele Mutation Model, |
| Events Allowed | Population Merge and Split, Varying Demographic Features, |
| Other | |
| Interface | Command-line, Script-based, |
| Development | |
| Tested Platforms | Mac OS X, Linux and Unix, |
| Language | C or C++, Python, |
| License | GNU Public License, |
| 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 FFPopSim.
2023
Latorre SM, Were VM, Foster AJ, Langner T, Malmgren A, Harant A, Asuke S, Reyes-Avila S, Gupta DR, Jensen C, et al., Genomic surveillance uncovers a pandemic clonal lineage of the wheat blast fungus., PLoS Biol, 04-11-2023 [Abstract]
2022
Stolyarova AV, Neretina TV, Zvyagina EA, Fedotova AV, Kondrashov AS, Bazykin GA, Complex fitness landscape shapes variation in a hyperpolymorphic species., Elife, 05-09-2022 [Abstract]