GSR: Simulator - SelSim
Attribute | Value |
---|---|
Title | SelSim |
Short Description | population genetic simulation (Not SelSim from Spencer & Coop 2004, which is currently unavailable) |
Long Description | With selsim, an evolving population of sequences is simulated according to a haploid Wright-Fisher model with discrete generations. This uses a Jukes-Cantor mutation model with a specified mutation rate. In each subsequent generation, the population is reconstituted by sampling sequences with replacement proportional to their frequency multiplied by their fitness. Mutations can be advantageous or deleterious and affect fitness in a multiplicative fashion (additive on a log-scale). Sequences are sampled at random time points after a period of burn-in. |
Version | 2.1 |
Last Release | 5 years, 7 months ago |
Homepage | https://github.com/trvrb/selsim |
Citations | Bedford T, Cobey S, Pascual M, Strength and tempo of selection revealed in viral gene genealogies., BMC Evol Biol, 07-25-2011 [ Abstract, cited in PMC ] |
GSR Certification | Accessibility |
Last evaluated | 04-27-2021 (1060 days ago) |
Author verification | The 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. |
Attribute Category | Attribute |
---|---|
Target | |
Type of Simulated Data | Haploid DNA Sequence, |
Variations | Single Nucleotide Variation, |
Simulation Method | Standard Coalescent, |
Input | |
Data Type | |
File format | |
Output | |
Data Type | Genotype or Sequence, Phenotypic Trait, |
Sequencing Reads | |
File Format | Other, |
Sample Type | Random or Independent, |
Phenotype | |
Trait Type | |
Determinants | |
Evolutionary Features | |
Demographic | |
Population Size Changes | Constant Size, |
Gene Flow | Continent-Island Models, |
Spatiality | |
Life Cycle | |
Mating System | Random Mating, |
Fecundity | |
Natural Selection | |
Determinant | Single-locus, |
Models | Directional Selection, Balancing Selection, |
Recombination | Uniform, Varying Recombination Rates, |
Mutation Models | Stepwise Mutation Model, |
Events Allowed | |
Other | |
Interface | Command-line, |
Development | |
Tested Platforms | Windows, Mac OS X, Linux and Unix, Solaris, |
Language | C or C++, |
License | GNU Public License, |
GSR Certification | Documentation, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using SelSim has been provided.
Please propose new citations if you are aware of publications that use this software.