GSR: Simulator - MetaPopGen
| Attribute | Value |
|---|---|
| Title | MetaPopGen |
| Short Description | Simulates genetics in large size metapopulations |
| Long Description | MetaPopGen is a population genetics simulator. Features included in the model are age-structure, monoecious and dioecious (or separate sexes) life-cycles, mutation, dispersal and selection. All demographic parameters can be genotype-, sex-, age-, deme- and time-dependent. MetaPopGen is therefore indicated to study large populations and very complex demographic scenarios. |
| Version | 2.0.0 |
| Project Started | 2014 |
| Last Release | 6 months ago |
| Homepage | https://github.com/MarcoAndrello/MetaPopGen |
| Citations |
|
| GSR Certification |  ✔ Accessibility |
| Last evaluated | 04-06-2021 (15 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Genotype at Genetic Markers, |
| Variations | Biallelic Marker, Multiallelic Marker, Single Nucleotide Variation, |
| Simulation Method | Forward-time, Other, |
| Input | |
| Data Type | Allele Frequencies, |
| File format | Program Specific, Other, |
| Output | |
| Data Type | Demographic, Diversity Measures, |
| Sequencing Reads | Other, |
| File Format | Program Specific, |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Carrying Capacity, User Defined, |
| Gene Flow | Island Models, User-defined Matrix, |
| Spatiality | |
| Life Cycle | Discrete Generation Model, Age structured, Overlapping Generation, User-Defined transition matrices, |
| Mating System | Random Mating, Selfing, |
| Fecundity | Constant Number, Randomly Distributed, Individually Determined, Influenced by Environment, |
| Natural Selection | |
| Determinant | Single-locus, Multi-locus, Environmental Factors, |
| Models | Multi-locus models, Other, |
| Recombination | |
| Mutation Models | k-Allele Model, |
| Events Allowed | Varying Demographic Features, |
| Other | |
| Interface | Command-line, Script-based, |
| Development | |
| Tested Platforms | Windows, |
| Language | R, |
| License | |
| GSR Certification | Accessibility, Documentation, Application, Support, |
The following 5 publications are selected examples of applications that used MetaPopGen.
2020
William Handal Claire Szostek Natalie Hold Marco Andrello Eric Thiébaut Ewan Harney Gwendoline Lefebvre Elodie Borcier Aurélie Jolivet Amandine Nicolle Aurélien Boyé Eric Foucher Pierre Boudry Grégory Charrier, New insights on the population genetic structure of the great scallop (Pecten maximus) in the English Channel, coupling microsatellite data and demogenetic simulations, Aquatic Conservation: marine and freshwater ecosystems, 09-04-2020 [Abstract]
Landguth EL, Forester BR, Eckert AJ, Shirk AJ, Menon M, Whipple A, Day CC, Cushman SA, Modelling multilocus selection in an individual-based, spatially-explicit landscape genetics framework., Mol Ecol Resour, 03-01-2020 [Abstract]
Smith AL, Hodkinson TR, Villellas J, Catford JA, Csergő AM, Blomberg SP, Crone EE, Ehrlén J, Garcia MB, Laine AL, et al., Global gene flow releases invasive plants from environmental constraints on genetic diversity., Proc Natl Acad Sci U S A, 02-25-2020 [Abstract]
2019
Claudio S. Quilodrán Kristen Ruegg Ashley T. Sendell‐Price Eric C. Anderson Tim Coulson Sonya M. Clegg, The multiple population genetic and demographic routes to islands of genomic divergence, Methods in Ecology and Evolution, 11-07-2019 [Abstract]
2017
Parobek CM, Archer FI, DePrenger-Levin ME, Hoban SM, Liggins L, Strand AE, skelesim: an extensible, general framework for population genetic simulation in R., Mol Ecol Resour, 01-01-2017 [Abstract]