GSR: Simulator - GenomePop2

Basic Package Attributes
AttributeValue
Title GenomePop2
Short Description GenomePop2 is a specialization of the program GenomePop just to manage SNPs under more flexible and useful settings. If you need models with more than 2 alleles please use the GenomePop program version.
Long Description This new version allows the forward simulation of sequences of biallelic positions. As in the previous version, a number of evolutionary and demographic settings are allowed. Several populations under any migration model can be implemented, contraction-expansion scenarios, directional or divergent selection. Theoretical or simulated initial equilibrium population can be computed the same as speciation processes via the simulation of user-defined population splits. Each population consists of a number N of individuals. Each individual is represented by one or more chromosomes with constant or variable (hotspots) recombination between binary sites.
Version 2.6.2
Project Started 2010
Last Release 5 years, 6 months ago
Homepagehttp://acraaj.webs.uvigo.es/GenomePop2.htm
Citations Carvajal-Rodríguez A, GENOMEPOP: a program to simulate genomes in populations., BMC Bioinformatics, 04-30-2008 [ Abstract, cited in PMC ]
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Last evaluated05-17-2018 (884 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, Mitochondrial DNA (Version 2.8 or later),
VariationsBiallelic Marker, Multiallelic Marker (The user only needs to define a given region without recombination (linked) and with a non-zero mutation rate ),
Simulation MethodForward-time,
Input
Data TypeAllele Frequencies (See howto 14 from the web page),
File formatOther (Fasta version 2.6 or later),
Output
Data TypeGenotype or Sequence,
Sequencing Reads
File FormatGenepop, MS, Phylip,
Sample TypeRandom or Independent (The user can define the population size and the sample size. ),
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Bottleneck, Carrying Capacity, User Defined,
Gene FlowStepping Stone Models, Island Models, Continent-Island Models, User-defined Matrix,
Spatiality
Life CycleDiscrete Generation Model,
Mating SystemRandom Mating, Polygamous (Depending on fitness as defined by the genotype), Selfing,
FecundityConstant Number, Individually Determined (Depending on fitness as defined by the genotype. ),
Natural Selection
DeterminantSingle-locus (User-defined), Multi-locus (User-defined),
ModelsDirectional Selection, Balancing Selection (User-defined via negative dominance coefficient), Multi-locus models, Random Fitness Effects,
RecombinationUniform, Varying Recombination Rates,
Mutation ModelsTwo-allele Mutation Model, Infinite-sites Model,
Events AllowedPopulation Merge and Split,
Other
InterfaceCommand-line, Graphical User Interface (Version 2.7 or later),
Development
Tested PlatformsWindows, Mac OS X, Linux and Unix,
LanguageC or C++, Java (For gui and from version 2.7 or later),
LicenseGNU Public License,
GSR CertificationDocumentation,

No example publication using GenomePop2 has been provided.

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