GSR: Simulator - Easypop

Basic Package Attributes
AttributeValue
Title Easypop
Short Description EASYPOP is an individual based model intended to simulate datasets under a very broad range of conditions
Long Description EASYPOP can simulate haploid, diploid or haplodiploid data. For diploids there is the choice between hermaphrodites or sexuals. For hermaphrodites, the proportion of clonal reproduction and selfing can be chosen, whereas for sexuals, complex breeding structures can be simulated (e.g. monogamy with a given proportion of extra-pair matings). The number of individuals can be selected for each population and dispersal is sex-specific. There are various migration models such as two-dimensional stepping stone or hierarchical island model. In addition there is an isolation-by-distance option which works with the coordinates of the populations on any number of dimensions. There are also several mutation models implemented, which are particularly oriented on the simulation of microsatellite loci. Genotypes are real multilocus, (i.e. there are not independent replicates for each locus). All mutation parameters can be set individually for each locus. EASYPOP is able to handle very large simulations on standard personal computers and is limited only by the memory of the machine. The computer code has been optimized for maximum speed. This allows running very large simulations on personal computers in a reasonable amount of time. In order to fit to analytical xpectations in particular for variances, the functions implemented in EASYPOP are probabilistic and not deterministic. In other words, the simulations rely on the genertation of random numbers.
Version 2.0.1
Project Started 2000
Last Release 14 years, 4 months ago
Homepagehttps://www.unil.ch/dee/en/home/menuinst/open-positions-and-public-resources/softwares--dataset/softwares/easypop.html
Citations Balloux F, EASYPOP (version 1.7): a computer program for population genetics simulations., J Hered, 05-01-2001 [ Abstract, cited in PMC ]
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Last evaluated07-12-2018 (827 days ago)
Author verificationThe basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator.
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataGenotype at Genetic Markers,
VariationsBiallelic Marker,
Simulation MethodForward-time,
Input
Data Type
File formatFstat, Genepop,
Output
Data TypeGenotype or Sequence, Diversity Measures,
Sequencing ReadsOther,
File FormatArlequin, Fstat, Genepop,
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size,
Gene FlowStepping Stone Models, Island Models,
Spatiality
Life Cycle
Mating SystemRandom Mating, Monogamous, Polygamous, Haplodiploid,
Fecundity
Natural Selection
Determinant
Models
RecombinationUniform, Varying Recombination Rates,
Mutation Modelsk-Allele Model, Stepwise Mutation Model,
Events AllowedVarying Demographic Features,
Other
InterfaceCommand-line,
Development
Tested PlatformsWindows, Mac OS X,
LanguageC or C++,
LicenseGNU Public License,
GSR CertificationDocumentation, Application,

The following 8 publications are selected examples of applications that used Easypop.

2017

Pelletier A, Obbard ME, Harnden M, McConnell S, Howe EJ, Burrows FG, White BN, Kyle CJ, Determining causes of genetic isolation in a large carnivore (Ursus americanus) population to direct contemporary conservation measures., PLoS One, 02-24-2017 [Abstract]

Kuismin MO, Ahlinder J, Sillanpӓӓ MJ, CONE: Community Oriented Network Estimation Is a Versatile Framework for Inferring Population Structure in Large-Scale Sequencing Data., G3 (Bethesda), 10-05-2017 [Abstract]

2016

Gracianne C, Jan PL, Fournet S, Olivier E, Arnaud JF, Porte C, Bardou-Valette S, Denis MC, Petit EJ, Temporal sampling helps unravel the genetic structure of naturally occurring populations of a phytoparasitic nematode. 2. Separating the relative effects of gene flow and genetic drift., Evol Appl, 07-22-2016 [Abstract]

Rojas-Hernandez N, Veliz D, Riveros MP, Fuentes JP, Pardo LM, Highly Connected Populations and Temporal Stability in Allelic Frequencies of a Harvested Crab from the Southern Pacific Coast., PLoS One, 11-04-2016 [Abstract]

2015

Guildea C, Hitchen Y, Duffy R, Dias PJ, Ledger JM, Snow M, Kennington WJ, Introgression threatens the survival of the critically endangered freshwater crayfish Cherax tenuimanus (Decapoda: Parastacidae) in the wild., PLoS One, 03-23-2015 [Abstract]

Parreira BR, Chikhi L, On some genetic consequences of social structure, mating systems, dispersal, and sampling., Proc Natl Acad Sci U S A, 06-30-2015 [Abstract]

Momigliano P, Harcourt R, Robbins WD, Stow A, Connectivity in grey reef sharks (Carcharhinus amblyrhynchos) determined using empirical and simulated genetic data., Sci Rep, 08-28-2015 [Abstract]

Kvistad L, Ingwersen D, Pavlova A, Bull JK, Sunnucks P, Very Low Population Structure in a Highly Mobile and Wide-Ranging Endangered Bird Species., PLoS One, 12-09-2015 [Abstract]


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