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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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