coala: A Framework for Coalescent Simulation (original) (raw)
Coalescent simulators can rapidly simulate biological sequences evolving according to a given model of evolution. You can use this package to specify such models, to conduct the simulations and to calculate additional statistics from the results (Staab, Metzler, 2016 <doi:10.1093/bioinformatics/btw098>). It relies on existing simulators for doing the simulation, and currently supports the programs 'ms', 'msms' and 'scrm'. It also supports finite-sites mutation models by combining the simulators with the program 'seq-gen'. Coala provides functions for calculating certain summary statistics, which can also be applied to actual biological data. One possibility to import data is through the 'PopGenome' package (<https://github.com/pievos101/PopGenome>).
| Version: | 0.7.2 |
|---|---|
| Depends: | R (≥ 3.1.0) |
| Imports: | assertthat (≥ 0.1), digest, methods, parallel, R6 (≥ 2.0.1), Rcpp (≥ 0.11.0), rehh (≥ 3.0.0), scrm (≥ 1.6.0-2), stats, utils |
| LinkingTo: | Rcpp, RcppArmadillo (≥ 0.3.810.0) |
| Suggests: | abc (≥ 2.0), knitr, PopGenome (≥ 2.1.0), phyclust (≥ 0.1-16), rmarkdown, testthat (≥ 0.11.0) |
| Published: | 2024-03-04 |
| DOI: | 10.32614/CRAN.package.coala |
| Author: | Paul Staab [aut], Dirk Metzler [aut, ths, cre], Jorge E. Amaya Romero [ctb] |
| Maintainer: | Dirk Metzler |
| BugReports: | https://github.com/statgenlmu/coala/issues |
| License: | MIT + file |
| URL: | https://github.com/statgenlmu/coala |
| NeedsCompilation: | yes |
| Citation: | coala citation info |
| Materials: | README, NEWS |
| CRAN checks: | coala results |
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