Calculate and Map Distances Between Phylogenetic Trees R package TreeDist version 2.14.1 CRAN Task View: Optimization (https://CRAN.R-project.org/view=Optimization) CRAN Task View: Phylogenetics (https://CRAN.R-project.org/view=Phylogenetics) 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>; the Hierarchical Mutual Information (Perotti et al. 2015) <doi:10.1103/PhysRevE.92.062825>; 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 identifying islands of trees (Silva and Wilkinson 2021) <doi:10.1093/sysbio/syab015>, for calculating the median of sets of trees, and for computing the information content of trees and splits. Software Depends: R (>= 4.0), stats, Imports: ape (>= 5.0), cli (>= 3.0), colorspace, Rdpack (>= 0.7), shiny, shinyjs, TreeTools (>= 2.1.0), LinkingTo: Rcpp, TreeTools (>= 2.1.0), Suggests: bookdown, cluster, ggplot2, hypervolume, kdensity, knitr, MASS, parallel, phangorn (>= 2.2.1), plotly, PlotTools, protoclust, Quartet, readxl, rmarkdown, Rcpp (>= 1.0.8), rgl, Rogue, spelling, TBRDist, testthat (>= 3.0), Ternary (>= 1.1.2), TreeDistData (> 0.1.0), TreeSearch (>= 1.4.0), Umatrix, vdiffr (>= 1.0.0), withr, Martin R. Smith <martin.smith@durham.ac.uk> Comprehensive R Archive Network (CRAN) Martin R. Smith [aut, cre, cph, prg] (ORCID: <https://orcid.org/0000-0001-5660-1727>), Roy Jonker [prg, cph] (LAP algorithm), Yong Yang [ctb, cph] (LAP algorithm), Yi Cao [ctb, cph] (LAP algorithm), Neil Kaye [cph] (Mercator image) GPL (>= 3) 2026-06-10 application/tgz https://CRAN.R-project.org/package=TreeDist doi:10.32614/CRAN.package.TreeDist en-GB