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 <> formats; and analysis of splits and cladistic information.

Version: 1.7.1
Depends: R (≥ 3.4.0), ape (≥ 5.6)
Imports: bit64, lifecycle, colorspace, fastmatch (≥ 1.1.3), methods, R.cache, Rdpack (≥ 2.2)
LinkingTo: Rcpp
Suggests: spelling, knitr, phangorn (≥ 2.2.1), Rcpp (≥ 1.0.8), rmarkdown, shiny, testthat (≥ 3.0), vdiffr (≥ 1.0.0)
Published: 2022-03-25
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: File system navigation in R
Loading phylogenetic data into R
Loading phylogenetic trees into R


Package source: TreeTools_1.7.1.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): TreeTools_1.7.1.tgz, r-release (x86_64): TreeTools_1.7.1.tgz, r-oldrel: TreeTools_1.7.1.tgz
Old sources: TreeTools archive

Reverse dependencies:

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


Please use the canonical form to link to this page.