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GSR: Simulator - santa-sim
| Attribute | Value |
|---|---|
| Title | santa-sim |
| Short Description | SANTA simulates the evolution of gene sequences. |
| Long Description | SANTA is JAVA software application that simulates the evolution of a population of gene sequences forwards through time. It models the underlying biological processes as discrete components; replication (including recombination), mutation (including indels), fitness and selection. SANTA is easy to use and is well-suited to simulate pathogen evolution according to different scenarios. |
| Version | v1.0 |
| Project Started | 2018 |
| Last Release | 7 years, 2 months ago |
| Homepage | https://github.com/santa-dev/santa-sim |
| Citations | Jariani A, Warth C, Deforche K, Libin P, Drummond AJ, Rambaut A, Matsen Iv FA, Theys K, SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination., Virus Evol, March 8, 2019 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | March 8, 2022 (1262 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 | Genotype at Genetic Markers, |
| Variations | |
| Simulation Method | Forward-time, |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | |
| Sequencing Reads | |
| File Format | |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | Directional Selection, Balancing Selection, |
| Recombination | Uniform, |
| Mutation Models | |
| Events Allowed | |
| Other | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | |
| 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 santa-sim.
2023
Jones BR, Joy JB, Inferring Human Immunodeficiency Virus 1 Proviral Integration Dates With Bayesian Inference., Mol Biol Evol, Aug. 3, 2023 [Abstract]
2022
Lytras S, Hughes J, Martin D, Swanepoel P, de Klerk A, Lourens R, Kosakovsky Pond SL, Xia W, Jiang X, Robertson DL, Exploring the Natural Origins of SARS-CoV-2 in the Light of Recombination., Genome Biol Evol, Feb. 4, 2022 [Abstract]