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 |