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) ; Jaccard-Robinson-Foulds distances (Bocker et al. 2013) , including the Nye et al. (2006) metric ; the Matching Split Distance (Bogdanowicz & Giaro 2012) ; Maximum Agreement Subtree distances; the Kendall-Colijn (2016) distance , and the Nearest Neighbour Interchange (NNI) distance, approximated per Li et al. (1996) . Includes tools for visualizing mappings of tree space, for calculating the median of sets of trees, and for computing the information content of trees and splits.


Reference manual

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2.2.0 by Martin R. Smith, 3 months ago,

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Authors: Martin R. Smith [aut, cre, cph, prg] , Roy Jonker [prg, cph] , Yong Yang [ctb, cph] , Yi Cao [ctb, cph]

Documentation:   PDF Manual  

GPL (>= 3) license

Imports ape, cli, colorspace, memoise, phangorn, Rdpack, shiny, shinyjs, TreeTools

Depends on stats

Suggests bookdown, cluster, ggplot2, kdensity, knitr, MASS, parallel, protoclust, Quartet, readxl, rmarkdown, Rcpp, rgl, testthat, Ternary, TreeDistData, TreeSearch, Umatrix, vdiffr

Linking to Rcpp, TreeTools

System requirements: C++14

Imported by Rogue, TBRDist, TreeSearch.

See at CRAN