Type: Package
Package: nodeSub
Title: Simulate DNA Alignments Using Node Substitutions
Version: 1.2.9
Authors@R: person(given = "Thijs",
                      family = "Janzen",
                      role = c("aut", "cre"),
                      email = "thijsjanzen@gmail.com")
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Description: 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>.
License: GPL-3
URL: https://github.com/thijsjanzen/nodeSub
BugReports: https://github.com/thijsjanzen/nodeSub/issues
Depends: ape, Rcpp
Imports: beastier, beautier, DDD, geiger, lifecycle, pbapply, phangorn,
        phylobase, rappdirs, Rmpfr, stringr, testit, tibble, tracerer
Suggests: dplyr, ggplot2, knitr, magrittr, nLTT, rmarkdown, RPANDA,
        testthat, tidyr, TreeSim
LinkingTo: Rcpp
VignetteBuilder: knitr
Encoding: UTF-8
RoxygenNote: 7.2.3
Config/pak/sysreqs: libglpk-dev libgmp3-dev make default-jdk libicu-dev
        libxml2-dev libmpfr-dev libssl-dev libx11-dev zlib1g-dev
Repository: https://phylotastic.r-universe.dev
Date/Publication: 2025-05-06 08:25:33 UTC
RemoteUrl: https://github.com/thijsjanzen/nodeSub
RemoteRef: HEAD
RemoteSha: 252d0658efaa9c8cb916a9dea64d3972c75e147e
NeedsCompilation: yes
Packaged: 2026-06-02 19:03:45 UTC; root
Author: Thijs Janzen [aut, cre]