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; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of node support; calculation of ancestor-descendant relationships; import and export of trees from Newick, Nexus (Maddison et al. 1997) <doi:10.1093/sysbio/46.4.590>, and TNT <> formats; and analysis of splits and cladistic information.

Version: 1.4.4
Depends: R (≥ 3.4.0), ape (≥ 5.0)
Imports: bit64, colorspace, phangorn (≥ 2.2.1), R.cache, Rdpack
LinkingTo: Rcpp
Suggests: knitr, Rcpp, rmarkdown, shiny, testthat, vdiffr
Published: 2021-04-20
Author: Martin R. Smith ORCID iD [aut, cre, cph], Emmanuel Paradis ORCID iD [cph]
Maintainer: Martin R. Smith <martin.smith at>
License: GPL (≥ 3)
Copyright: Incorporates C/C++ code from 'ape' by Emmanuel Paradis <doi:10.1093/bioinformatics/bty633>
NeedsCompilation: yes
SystemRequirements: C++14
Language: en-GB
Citation: TreeTools citation info
Materials: NEWS
CRAN checks: TreeTools results


Reference manual: TreeTools.pdf
Vignettes: Navigating the file system in R
Load phylogenetic data
Load phylogenetic trees
Package source: TreeTools_1.4.4.tar.gz
Windows binaries: r-devel:, r-devel-UCRT:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): TreeTools_1.4.4.tgz, r-release (x86_64): TreeTools_1.4.4.tgz, r-oldrel: TreeTools_1.4.4.tgz
Old sources: TreeTools archive

Reverse dependencies:

Reverse imports: Quartet, TBRDist, TotalCopheneticIndex, TreeDist, TreeSearch
Reverse linking to: TreeDist


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