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: 1.14.0 Depends: R (≥ 3.4.0), ape (≥ 5.6) Imports: bit64, lifecycle, colorspace, fastmatch (≥ 1.1.3), methods, PlotTools, RCurl, R.cache, Rdpack (≥ 2.3) LinkingTo: Rcpp Suggests: spelling, knitr, phangorn (≥ 2.2.1), purrr, Rcpp (≥ 1.0.8), rlang, rmarkdown, testthat (≥ 3.0), vdiffr (≥ 1.0.0) Published: 2025-05-13 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: Downloads: Reverse dependencies: Linking:Please use the canonical form https://CRAN.R-project.org/package=TreeTools to link to this page.
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