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TreeTools: Create, Modify and Analyse Phylogenetic Trees

Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; tree rearrangement; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of split support; plotting the position of rogue taxa (Klopfstein & Spasojevic 2019) <doi:10.1371/journal.pone.0212942>; calculation of ancestor-descendant relationships, of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>, and of tree balance (Mir et al. 2013, Lemant et al. 2022) <doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>; artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>; import and export of trees from Newick, Nexus (Maddison et al. 1997) <doi:10.1093/sysbio/46.4.590>, and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats; and analysis of splits and cladistic information.

Version: 1.12.0
Depends: R (≥ 3.4.0), ape (≥ 5.6)
Imports: bit64, lifecycle, colorspace, fastmatch (≥ 1.1.3), methods, PlotTools, RCurl, R.cache, Rdpack (≥ 2.3)
LinkingTo: Rcpp
Suggests: spelling, knitr, phangorn (≥ 2.2.1), purrr, Rcpp (≥ 1.0.8), rlang, rmarkdown, testthat (≥ 3.0), vdiffr (≥ 1.0.0)
Published: 2024-07-25
DOI: 10.32614/CRAN.package.TreeTools
Author: Martin R. Smith ORCID iD [aut, cre, cph], Emmanuel Paradis ORCID iD [cph], Robert Noble ORCID iD [cph]
Maintainer: Martin R. Smith <martin.smith at durham.ac.uk>
BugReports: https://github.com/ms609/TreeTools/issues/
License: GPL (≥ 3)
Copyright: Incorporates C/C++ code from 'ape' by Emmanuel Paradis <doi:10.1093/bioinformatics/bty633> and 'RUtreebalance' by Robert Noble <doi:10.5281/zenodo.5873857>.
URL: https://ms609.github.io/TreeTools/, https://github.com/ms609/TreeTools/
NeedsCompilation: yes
SystemRequirements: C++17
Language: en-GB
Citation: TreeTools citation info
Materials: NEWS
In views: Phylogenetics
CRAN checks: TreeTools results

Documentation:

Reference manual: TreeTools.pdf
Vignettes: File system navigation in R
Loading phylogenetic data into R
Loading phylogenetic trees into R

Downloads:

Package source: TreeTools_1.12.0.tar.gz
Windows binaries: r-devel: TreeTools_1.12.0.zip, r-release: TreeTools_1.12.0.zip, r-oldrel: TreeTools_1.12.0.zip
macOS binaries: r-release (arm64): TreeTools_1.12.0.tgz, r-oldrel (arm64): TreeTools_1.12.0.tgz, r-release (x86_64): TreeTools_1.12.0.tgz, r-oldrel (x86_64): TreeTools_1.12.0.tgz
Old sources: TreeTools archive

Reverse dependencies:

Reverse depends: Quartet
Reverse imports: avotrex, orthGS, Rogue, TBRDist, TotalCopheneticIndex, TreeDist, TreeSearch
Reverse linking to: TreeDist, TreeSearch
Reverse suggests: orthogene, phylosem

Linking:

Please use the canonical form https://CRAN.R-project.org/package=TreeTools to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.