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: | 2.0.0 |
| Depends: | R (≥ 3.6.0), ape (≥ 5.6) |
| Imports: | bit64, fastmatch (≥ 1.1.3), methods, PlotTools, RCurl, Rdpack (≥ 2.3), stringi |
| LinkingTo: | Rcpp |
| Suggests: | spelling, knitr, phangorn (≥ 2.2.1), Rcpp (≥ 1.0.8), rmarkdown, testthat (≥ 3.0), TreeDist, TreeSearch, vdiffr (≥ 1.0.0) |
| Published: | 2025-09-23 |
| DOI: | 10.32614/CRAN.package.TreeTools |
| Author: | Martin R. Smith 
[aut, cre, cph],
Emmanuel Paradis
[cph],
Robert Noble
[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.html , TreeTools.pdf |
| Vignettes: |
File system navigation in R (source) Loading phylogenetic data into R (source, R code) Loading phylogenetic trees into R (source, R code) |
Downloads:
| Package source: | TreeTools_2.0.0.tar.gz |
| Windows binaries: | r-devel: TreeTools_2.0.0.zip, r-release: TreeTools_2.0.0.zip, r-oldrel: TreeTools_2.0.0.zip |
| macOS binaries: | r-release (arm64): TreeTools_2.0.0.tgz, r-oldrel (arm64): TreeTools_2.0.0.tgz, r-release (x86_64): TreeTools_2.0.0.tgz, r-oldrel (x86_64): TreeTools_2.0.0.tgz |
| Old sources: | TreeTools archive |
Reverse dependencies:
| Reverse depends: | Quartet |
| Reverse imports: | avotrex, BAT, 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.