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GSR: Simulator - phylodyn
| Attribute | Value |
|---|---|
| Title | phylodyn |
| Short Description | Phylodyn facilitates phylodynamic inference and analysis in an approachable R package. |
| Long Description | Phylon is an r package for phylodynamic analysis based on gene genealogies. The package applies Bayesian nonparametric estimation for population size fluctuations over time. The software includes Markov chain Monte Carlo-based methods and an integrated nested Laplace approximation-based approach for phylodynamic inference. The genealogical data describes the timed ancestral relationships of individuals sampled from a population of interest. The individuals within the software are simulated according to isochronous sampling or heterochronous sampling. The purpose of phylodyn is to fascilitate phylodynamic inference and analysis in an approachable R package. |
| Version | 0.9.0 |
| Project Started | 2019 |
| Last Release | 6 years, 3 months ago |
| Homepage | https://github.com/mdkarcher/phylodyn |
| Citations | Karcher MD, Palacios JA, Lan S, Minin VN, phylodyn: an R package for phylodynamic simulation and inference., Mol Ecol Resour, Jan. 1, 2017 [ Abstract, cited in PMC ] |
| GSR Certification | Accessibility |
| Last evaluated | May 17, 2022 (1193 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 | Standard Coalescent, |
| 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 | Mac OS X, Linux and Unix, |
| Language | R, |
| License | Other, |
| GSR Certification | Documentation, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used phylodyn.
2023
Hamede R, Fountain-Jones NM, Arce F, Jones M, Storfer A, Hohenlohe PA, McCallum H, Roche B, Ujvari B, Thomas F, The tumour is in the detail: Local phylogenetic, population and epidemiological dynamics of a transmissible cancer in Tasmanian devils., Evol Appl, June 20, 2023 [Abstract]
2022
Featherstone LA, Zhang JM, Vaughan TG, Duchene S, Epidemiological inference from pathogen genomes: A review of phylodynamic models and applications., Virus Evol, June 2, 2022 [Abstract]