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GSR: Simulator - Coala
| Attribute | Value |
|---|---|
| Title | Coala |
| Short Description | Coala is an R package that simulates biological sequences according to a given model of evolution. |
| Long Description | Coala is an R package that simulates biological sequences according to a given model of evolution. The package calls simulators based on coalescent theory. All the simulators can simulate finite site mutation models when combined with Seq-gen. Coala then imports the output of the simulators into R and is capable of calculating their summary statistics. |
| Version | 0.6.1 |
| Project Started | 2015 |
| Last Release | 3 years, 6 months ago |
| Homepage | https://github.com/statgenlmu/coala |
| Citations | Staab PR, Metzler D, Coala: an R framework for coalescent simulation., Bioinformatics, June 15, 2016 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | May 17, 2022 (1192 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, Haploid DNA Sequence, |
| Variations | |
| Simulation Method | Standard Coalescent, Exact 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 | Constant Size, Exponential Growth or Decline, Bottleneck, |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | Single-locus, |
| 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 | Accessibility, 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 Coala.
2022
Lees JA, Tonkin-Hill G, Yang Z, Corander J, Mandrake: visualizing microbial population structure by embedding millions of genomes into a low-dimensional representation., Philos Trans R Soc Lond B Biol Sci, Oct. 10, 2022 [Abstract]
Tricou T, Tannier E, de Vienne DM, Ghost lineages can invalidate or even reverse findings regarding gene flow., PLoS Biol, Sept. 14, 2022 [Abstract]
2020
Setter D, Mousset S, Cheng X, Nielsen R, DeGiorgio M, Hermisson J, VolcanoFinder: Genomic scans for adaptive introgression., PLoS Genet, June 18, 2020 [Abstract]