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: |
1.2.8 |
| Depends: |
Rcpp, ape |
| Imports: |
phangorn, tibble, DDD, Rmpfr, pbapply, phylobase, geiger, beautier, beastier, tracerer, rappdirs, testit, stringr, lifecycle |
| LinkingTo: |
Rcpp |
| Suggests: |
testthat, TreeSim, dplyr, knitr, rmarkdown, ggplot2, magrittr, tidyr, nLTT, RPANDA |
| Published: |
2023-11-14 |
| DOI: |
10.32614/CRAN.package.nodeSub |
| Author: |
Thijs Janzen |
| Maintainer: |
Thijs Janzen <thijsjanzen at gmail.com> |
| BugReports: |
https://github.com/thijsjanzen/nodeSub |
| License: |
GPL-3 |
| URL: |
https://github.com/thijsjanzen/nodeSub |
| NeedsCompilation: |
yes |
| Materials: |
README |
| CRAN checks: |
nodeSub results |
Documentation:
Downloads:
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