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>
License: GPL-3
NeedsCompilation: yes
Materials: README
CRAN checks: nodeSub results


Reference manual: nodeSub.pdf
Vignettes: substitution_models


Package source: nodeSub_1.2.8.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): nodeSub_1.2.8.tgz, r-oldrel (arm64): nodeSub_1.2.8.tgz, r-release (x86_64): nodeSub_1.2.8.tgz, r-oldrel (x86_64): nodeSub_1.2.8.tgz
Old sources: nodeSub archive


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