An official website of the United States government
GSR: Simulator - CoreSimul
| Attribute | Value |
|---|---|
| Title | CoreSimul |
| Short Description | a forward-in-time simulator of genome evolution for prokaryotes modeling homologous recombination |
| Long Description | CoreSimul is a forward-in-time simulator of core genome evolution for prokaryotes modeling homologous recombination. Simulations are guided by a phylogenetic tree and incorporate different substitution models, including models of codon selection. |
| Last Release | 5 years, 3 months ago |
| Homepage | https://github.com/lbobay/CoreSimul |
| Citations | Bobay LM, CoreSimul: a forward-in-time simulator of genome evolution for prokaryotes modeling homologous recombination., BMC Bioinformatics, June 24, 2020 [ Abstract, cited in PMC ] |
| GSR Certification | Accessibility |
| Last evaluated | Sept. 30, 2021 (1422 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 | Single Nucleotide Variation, |
| 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 | Single-locus, |
| Models | |
| Recombination | Uniform, |
| Mutation Models | |
| Events Allowed | |
| Other | |
| Interface | |
| Development | |
| Tested Platforms | |
| Language | Python, |
| License | |
| GSR Certification | Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 3
The following 3 publications are selected examples of applications that used CoreSimul.
2022
Diop A, Torrance EL, Stott CM, Bobay LM, Gene flow and introgression are pervasive forces shaping the evolution of bacterial species., Genome Biol, Nov. 10, 2022 [Abstract]
2020
Stott CM, Bobay LM, Impact of homologous recombination on core genome phylogenies., BMC Genomics, Nov. 25, 2020 [Abstract]
Bobay LM, O'Donnell AC, Ochman H, Recombination events are concentrated in the spike protein region of Betacoronaviruses., PLoS Genet, Dec. 17, 2020 [Abstract]