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, 2021) <doi:10.1093/sysbio/syab072>, and of tree balance (Mir et al. 2013) <doi:10.1016/j.mbs.2012.10.005>; 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 <http://www.lillo.org.ar/phylogeny/tnt/> formats; and analysis of splits and cladistic information.

Version: 1.7.2
Depends: R (≥ 3.4.0), ape (≥ 5.6)
Imports: bit64, lifecycle, colorspace, fastmatch (≥ 1.1.3), methods, R.cache, Rdpack (≥ 2.3)
LinkingTo: Rcpp
Suggests: spelling, knitr, phangorn (≥ 2.2.1), Rcpp (≥ 1.0.8), rmarkdown, shiny, testthat (≥ 3.0), vdiffr (≥ 1.0.0)
Published: 2022-05-24
Author: Martin R. Smith ORCID iD [aut, cre, cph], Emmanuel Paradis 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>
URL: https://ms609.github.io/TreeTools/, https://github.com/ms609/TreeTools/
NeedsCompilation: yes
SystemRequirements: C++14
Language: en-GB
Citation: TreeTools citation info
Materials: NEWS
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_1.7.2.tar.gz
Windows binaries: r-devel: TreeTools_1.7.2.zip, r-release: TreeTools_1.7.2.zip, r-oldrel: TreeTools_1.7.1.zip
macOS binaries: r-release (arm64): TreeTools_1.7.2.tgz, r-oldrel (arm64): TreeTools_1.7.2.tgz, r-release (x86_64): TreeTools_1.7.2.tgz, r-oldrel (x86_64): TreeTools_1.7.2.tgz
Old sources: TreeTools archive

Reverse dependencies:

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

Linking:

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