GSR: Simulator - MetaPopGen

Basic Package Attributes
AttributeValue
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
Homepagehttps://github.com/MarcoAndrello/MetaPopGen
Citations
  • Andrello M, Noirot C, Débarre F, Manel S, MetaPopGen 2.0: A multilocus genetic simulator to model populations of large size., Mol Ecol Resour, 02-01-2021 [ Abstract , cited in PMC ]
  • Andrello M, Manel S, MetaPopGen: an r package to simulate population genetics in large size metapopulations., Mol Ecol Resour, 01-13-2015 [ Abstract , cited in PMC ]
GSR CertificationGSR-certified

Accessibility
Documentation
Application
Support

Last evaluated04-06-2021 (15 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataGenotype at Genetic Markers,
VariationsBiallelic Marker, Multiallelic Marker, Single Nucleotide Variation,
Simulation MethodForward-time, Other,
Input
Data TypeAllele Frequencies,
File formatProgram Specific, Other,
Output
Data TypeDemographic, Diversity Measures,
Sequencing ReadsOther,
File FormatProgram Specific,
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Carrying Capacity, User Defined,
Gene FlowIsland Models, User-defined Matrix,
Spatiality
Life CycleDiscrete Generation Model, Age structured, Overlapping Generation, User-Defined transition matrices,
Mating SystemRandom Mating, Selfing,
FecundityConstant Number, Randomly Distributed, Individually Determined, Influenced by Environment,
Natural Selection
DeterminantSingle-locus, Multi-locus, Environmental Factors,
ModelsMulti-locus models, Other,
Recombination
Mutation Modelsk-Allele Model,
Events AllowedVarying Demographic Features,
Other
InterfaceCommand-line, Script-based,
Development
Tested PlatformsWindows,
LanguageR,
License
GSR CertificationAccessibility, 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]


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