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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 <metzler at bio.lmu.de> |
| BugReports: | https://github.com/statgenlmu/coala/issues |
| License: | MIT + file LICENSE |
| URL: | https://github.com/statgenlmu/coala |
| NeedsCompilation: | yes |
| Citation: | coala citation info |
| Materials: | README NEWS |
| CRAN checks: | coala results |
| Package source: | coala_0.7.2.tar.gz |
| Windows binaries: | r-devel: coala_0.7.2.zip, r-release: coala_0.7.2.zip, r-oldrel: coala_0.7.2.zip |
| macOS binaries: | r-release (arm64): coala_0.7.2.tgz, r-oldrel (arm64): coala_0.7.2.tgz, r-release (x86_64): coala_0.7.2.tgz, r-oldrel (x86_64): coala_0.7.2.tgz |
| Old sources: | coala archive |
| Reverse suggests: | jaatha, jackalope |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.