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. The nodeSub 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:10.1101/2020.08.19.256891>.

Version: 1.2
Depends: Rcpp
Imports: nLTT, RPANDA, apTreeshape, phangorn, tibble, DDD, Rmpfr, assertthat, pbapply, phylobase, rappdirs, stringr, geiger, ape, testit, babette, beautier, beastier, mauricer, tracerer
LinkingTo: Rcpp
Suggests: phytools, testthat, TreeSim, dplyr, knitr, rmarkdown, ggplot2, magrittr, tidyr
Published: 2021-09-30
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:

Reference manual: nodeSub.pdf
Vignettes: substitution_models
workflow

Downloads:

Package source: nodeSub_1.2.tar.gz
Windows binaries: r-devel: nodeSub_1.2.zip, r-release: nodeSub_1.2.zip, r-oldrel: nodeSub_1.2.zip
macOS binaries: r-release (arm64): nodeSub_1.2.tgz, r-release (x86_64): nodeSub_1.2.tgz, r-oldrel: nodeSub_1.2.tgz

Linking:

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