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GSR: Simulator - Pyvolve
| Attribute | Value |
|---|---|
| Title | Pyvolve |
| Short Description | A Flexible Python Module for Simulating Sequences along Phylogenies |
| Long Description | Pyvolve is an open-source Python module for simulating sequences along a phylogenetic tree according to continuous-time Markov models of sequence evolution. |
| Version | 1.0.3 |
| Project Started | 2009 |
| Last Release | 5 years, 11 months ago |
| Homepage | https://github.com/sjspielman/pyvolve |
| Citations | Spielman SJ, Wilke CO, Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies., PLoS One, Sept. 23, 2015 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | June 10, 2021 (1976 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 | |
| Variations | |
| Simulation Method | |
| 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 | |
| Development | |
| Tested Platforms | |
| Language | |
| 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 Pyvolve.
2023
Zhai H, Fukuyama J, A convenient correspondence between k-mer-based metagenomic distances and phylogenetically-informed β-diversity measures., PLoS Comput Biol, Jan. 6, 2023 [Abstract]
2022
Guo F, Carbone I, Rasmussen DA, Recombination-aware phylogeographic inference using the structured coalescent with ancestral recombination., PLoS Comput Biol, Aug. 19, 2022 [Abstract]