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GSR: Simulator - GenPhyloData
| Attribute | Value |
|---|---|
| Title | GenPhyloData |
| Short Description | realistic simulation of gene family evolution |
| Long Description | PrIME-GenPhyloData is a suite of tools for creating realistic simulated phylogenetic trees, in particular for families of homologous genes. It supports generation of trees based on a birth-death process and—perhaps more interestingly—also supports generation of gene family trees guided by a known (synthetic or biological) species tree while accounting for events such as gene duplication, gene loss, and lateral gene transfer (LGT). The suite also supports a wide range of branch rate models enabling relaxation of the molecular clock. |
| Homepage | https://code.google.com/p/jprime/ |
| Citations | Sjöstrand J, Arvestad L, Lagergren J, Sennblad B, GenPhyloData: realistic simulation of gene family evolution., BMC Bioinformatics, June 27, 2013 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | May 15, 2023 (852 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 | Diploid DNA Sequence, |
| Variations | |
| Simulation Method | Resample Existing Data, |
| 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 | BSD, |
| 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 GenPhyloData.
2022
Jarvis DE, Maughan PJ, DeTemple J, Mosquera V, Li Z, Barker MS, Johnson LA, Whipple CJ, Chromosome-Scale Genome Assembly of Gilia yorkii Enables Genetic Mapping of Floral Traits in an Interspecies Cross., Genome Biol Evol, March 2, 2022 [Abstract]
Pelosi JA, Kim EH, Barbazuk WB, Sessa EB, Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns., Front Plant Sci, July 14, 2022 [Abstract]