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GSR: Simulator - ARGON
| Attribute | Value |
|---|---|
| Title | ARGON |
| Short Description | Fast, whole-genome simulation of the discrete time Wright-Fisher process |
| Long Description | ARGON simulates the discrete time Wright Fisher process (DTWF) backwards in time. The coalescent is equivalent to the DTWF process if the sample size is small compared to the effective population size, but will deviate from it as the sample size increases (Wakeley and Takahashi, MBE 2003; Bhaskar, Clark and Song, PNAS 2014). ARGON supports arbitrary demographic history, migration, variable mutation/recombination rates and gene conversion, and efficiently outputs pairwise identical-by-descent (IBD) sharing data. |
| Version | 0.1.160415 |
| Last Release | 8 years ago |
| Homepage | https://github.com/pierpal/ARGON |
| Citations | Palamara PF, ARGON: fast, whole-genome simulation of the discrete time Wright-fisher process., Bioinformatics, 10-01-2016 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | 07-08-2021 (1010 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 | Exact Coalescent, |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | Genotype or Sequence, |
| Sequencing Reads | |
| File Format | VCF, |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Exponential Growth or Decline, Logistic Growth, Bottleneck, Carrying Capacity, User Defined, |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | Uniform, Varying Recombination Rates, |
| Mutation Models | |
| Events Allowed | |
| Other | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, |
| Language | Java, |
| License | |
| GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used ARGON.
2022
Baumdicker F, Bisschop G, Goldstein D, Gower G, Ragsdale AP, Tsambos G, Zhu S, Eldon B, Ellerman EC, Galloway JG, et al., Efficient ancestry and mutation simulation with msprime 1.0., Genetics, 03-03-2022 [Abstract]
2021
Fitak RR, OptM: estimating the optimal number of migration edges on population trees using Treemix., Biol Methods Protoc, 09-16-2021 [Abstract]