TreeDist: Calculate and Map Distances Between Phylogenetic Trees

Implements measures of tree similarity, including information-based generalized Robinson-Foulds distances (Phylogenetic Information Distance, Clustering Information Distance, Matching Split Information Distance; Smith 2020) <doi:10.1093/bioinformatics/btaa614>; Jaccard-Robinson-Foulds distances (Bocker et al. 2013) <doi:10.1007/978-3-642-40453-5_13>, including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>; the Matching Split Distance (Bogdanowicz & Giaro 2012) <doi:10.1109/TCBB.2011.48>; Maximum Agreement Subtree distances; the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the Nearest Neighbour Interchange (NNI) distance, approximated per Li et al. (1996) <doi:10.1007/3-540-61332-3_168>. Includes tools for visualizing mappings of tree space (Smith 2022) <doi:10.1093/sysbio/syab100>, for calculating the median of sets of trees, and for computing the information content of trees and splits.

Version: 2.5.0
Depends: R (≥ 3.4.0), stats
Imports: ape (≥ 5.0), cli (≥ 3.0), colorspace, memoise, phangorn (≥ 2.2.1), Rdpack (≥ 0.7), shiny, shinyjs, TreeTools (≥
LinkingTo: Rcpp, TreeTools
Suggests: bookdown, cluster, ggplot2, hypervolume, kdensity, knitr, MASS, parallel, plotly, protoclust, Quartet, readxl, rmarkdown, Rcpp (≥ 1.0.8), rgl, Rogue, spelling, testthat (≥ 3.0), Ternary (≥ 1.1.2), TreeDistData (> 0.1.0), TreeSearch, Umatrix, uwot, vdiffr (≥ 1.0.0)
Published: 2022-10-07
Author: Martin R. Smith ORCID iD [aut, cre, cph, prg], Roy Jonker [prg, cph], Yong Yang [ctb, cph], Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith at>
License: GPL (≥ 3)
Copyright: Jonker-Volgenant Linear Assignment Problem implementation by Roy Jonker modified by Yong Yang and Yi Cao.
NeedsCompilation: yes
SystemRequirements: C++14
Language: en-GB
Citation: TreeDist citation info
Materials: NEWS
In views: Phylogenetics
CRAN checks: TreeDist results


Reference manual: TreeDist.pdf
Vignettes: Generalized Robinson-Foulds distances
Extending the Robinson-Foulds metric
Calculate tree similarity with 'TreeDist'
Comparing sets of trees from different analyses
Comparing splits using information theory
Analysing landscapes of phylogenetic trees
Tree space analysis
Contextualizing tree distances


Package source: TreeDist_2.5.0.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): TreeDist_2.5.0.tgz, r-oldrel (arm64): TreeDist_2.5.0.tgz, r-release (x86_64): TreeDist_2.5.0.tgz, r-oldrel (x86_64): TreeDist_2.5.0.tgz
Old sources: TreeDist archive

Reverse dependencies:

Reverse imports: Rogue, TBRDist, TreeSearch


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