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, 06-27-2013 [ Abstract, cited in PMC ] |
GSR Certification | ✔ Accessibility |
Last evaluated | 05-15-2023 (334 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, 03-02-2022 [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, 07-14-2022 [Abstract]