Create, Modify and Analyse Phylogenetic Trees R package TreeTools version 2.4.0 CRAN Task View: Phylogenetics (https://CRAN.R-project.org/view=Phylogenetics) 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. Software Depends: R (>= 3.6.0), ape (>= 5.6), Imports: bit64, fastmatch (>= 1.1.3), methods, PlotTools, Rdpack (>= 2.6.6), LinkingTo: Rcpp Suggests: RCurl, spelling, knitr, phangorn (>= 2.2.1), Rcpp (>= 1.0.8), rmarkdown, testthat (>= 3.0), TreeDist, TreeSearch, vdiffr (>= 1.0.0), Martin R. Smith <martin.smith@durham.ac.uk> Comprehensive R Archive Network (CRAN) Martin R. Smith [aut, cre, cph] (ORCID: <https://orcid.org/0000-0001-5660-1727>), Emmanuel Paradis [cph] (ORCID: <https://orcid.org/0000-0003-3092-2199>, ape library), Robert Noble [cph] (ORCID: <https://orcid.org/0000-0002-8057-4252>, RUtreebalance) GPL (>= 3) 2026-06-02 application/tgz https://CRAN.R-project.org/package=TreeTools doi:10.32614/CRAN.package.TreeTools en-GB