nodeSub: Simulate DNA Alignments Using Node Substitutions
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 <thijsjanzen at gmail.com> |
| BugReports: |
https://github.com/thijsjanzen/nodeSub/issues |
| License: |
GPL-3 |
| URL: |
https://github.com/thijsjanzen/nodeSub |
| NeedsCompilation: |
yes |
| Materials: |
README |
| CRAN checks: |
nodeSub results |
Documentation:
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