nodeSub: Simulate DNA Alignments Using Node Substitutions (original) (raw)
Simulate DNA sequences for the node substitution model. In the node substitution model, substitutions accumulate additionally during a speciation event, providing a potential mechanistic explanation for substitution rate variation. This package provides tools to simulate such a process, simulate a reference process with only substitutions along the branches, and provides tools to infer phylogenies from alignments. More information can be found in Janzen (2021) <doi:10.1093/sysbio/syab085>.
| Version: | 1.2.9 |
|---|---|
| Depends: | ape, Rcpp |
| Imports: | beastier, beautier, DDD, geiger, lifecycle, pbapply, phangorn, phylobase, rappdirs, Rmpfr, stringr, testit, tibble, tracerer |
| LinkingTo: | Rcpp |
| Suggests: | dplyr, ggplot2, knitr, magrittr, nLTT, rmarkdown, RPANDA, testthat, tidyr, TreeSim |
| Published: | 2025-05-06 |
| DOI: | 10.32614/CRAN.package.nodeSub |
| Author: | Thijs Janzen [aut, cre] |
| Maintainer: | Thijs Janzen |
| BugReports: | https://github.com/thijsjanzen/nodeSub/issues |
| License: | GPL-3 |
| URL: | https://github.com/thijsjanzen/nodeSub |
| NeedsCompilation: | yes |
| Materials: | README |
| CRAN checks: | nodeSub results |
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