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, 1 month 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 (1138 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]