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GSR: Simulator - VirusTreeSimulator
| Attribute | Value |
|---|---|
| Title | VirusTreeSimulator |
| Short Description | Simulates virus trees within a given transmission tree |
| Long Description | Simulates virus trees within a given transmission tree |
| Project Started | 2014 |
| Last Release | 5 years, 10 months ago |
| Homepage | https://github.com/PangeaHIV/VirusTreeSimulator |
| Citations | |
| GSR Certification | ✔ Accessibility |
| Last evaluated | May 15, 2023 (853 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 | |
| Simulation Method | Phylogenetic, |
| 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 | |
| Recombination | |
| Mutation Models | |
| Events Allowed | |
| Other | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | |
| Language | Java, |
| License | GNU Public License, |
| GSR Certification | Accessibility, |
Number of Primary Citations: 0
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used VirusTreeSimulator.
2019
Moshiri N, Ragonnet-Cronin M, Wertheim JO, Mirarab S, FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences., Bioinformatics, June 1, 2019 [Abstract]
2017
Ratmann O, Hodcroft EB, Pickles M, Cori A, Hall M, Lycett S, Colijn C, Dearlove B, Didelot X, Frost S, et al., Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison., Mol Biol Evol, Jan. 1, 2017 [Abstract]