GSR: Simulator - GenomePop2
Attribute | Value |
---|---|
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 | 9 years ago |
Homepage | http://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 ] |
GSR Certification | Accessibility |
Last evaluated | 05-17-2018 (2158 days ago) |
Attribute Category | Attribute |
---|---|
Target | |
Type of Simulated Data | Genotype at Genetic Markers, Mitochondrial DNA (Version 2.8 or later), |
Variations | Biallelic Marker, Multiallelic Marker (The user only needs to define a given region without recombination (linked) and with a non-zero mutation rate ), |
Simulation Method | Forward-time, |
Input | |
Data Type | Allele Frequencies (See howto 14 from the web page), |
File format | Other (Fasta version 2.6 or later), |
Output | |
Data Type | Genotype or Sequence, |
Sequencing Reads | |
File Format | Genepop, MS, Phylip, |
Sample Type | Random or Independent (The user can define the population size and the sample size. ), |
Phenotype | |
Trait Type | |
Determinants | |
Evolutionary Features | |
Demographic | |
Population Size Changes | Constant Size, Bottleneck, Carrying Capacity, User Defined, |
Gene Flow | Stepping Stone Models, Island Models, Continent-Island Models, User-defined Matrix, |
Spatiality | |
Life Cycle | Discrete Generation Model, |
Mating System | Random Mating, Polygamous (Depending on fitness as defined by the genotype), Selfing, |
Fecundity | Constant Number, Individually Determined (Depending on fitness as defined by the genotype. ), |
Natural Selection | |
Determinant | Single-locus (User-defined), Multi-locus (User-defined), |
Models | Directional Selection, Balancing Selection (User-defined via negative dominance coefficient), Multi-locus models, Random Fitness Effects, |
Recombination | Uniform, Varying Recombination Rates, |
Mutation Models | Two-allele Mutation Model, Infinite-sites Model, |
Events Allowed | Population Merge and Split, |
Other | |
Interface | Command-line, Graphical User Interface (Version 2.7 or later), |
Development | |
Tested Platforms | Windows, Mac OS X, Linux and Unix, |
Language | C or C++, Java (For gui and from version 2.7 or later), |
License | GNU Public License, |
GSR Certification | Documentation, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using GenomePop2 has been provided.
Please propose new citations if you are aware of publications that use this software.