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:

Reference manual:	nodeSub.pdf
Vignettes:	substitution_models

Downloads:

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