GSR: Simulator - santa-sim

Basic Package Attributes
AttributeValue
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
Homepagehttps://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 CertificationGSR-certified

Accessibility
Documentation
Application
Support

Last evaluatedMarch 8, 2022 (1138 days ago)
Author verificationThe 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.
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataGenotype at Genetic Markers,
Variations
Simulation MethodForward-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
ModelsDirectional Selection, Balancing Selection,
RecombinationUniform,
Mutation Models
Events Allowed
Other
InterfaceCommand-line,
Development
Tested Platforms
LanguageJava,
License
GSR CertificationAccessibility, 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]


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