TreeTools: Create, Modify and Analyse Phylogenetic Trees

Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of node support; calculation of ancestor-descendant relationships; import and export of trees from Newick, Nexus (Maddison et al. 1997) <doi:10.1093/sysbio/46.4.590>, and TNT <http://www.lillo.org.ar/phylogeny/tnt/> formats; and analysis of splits and cladistic information.

Version: 1.3.0
Depends: R (≥ 3.4.0), ape (≥ 5.0)
Imports: bit64, colorspace, phangorn (≥ 2.2.1), R.cache, Rdpack
LinkingTo: Rcpp
Suggests: knitr, Rcpp, rmarkdown, shiny, testthat, vdiffr
Published: 2020-09-22
Author: Martin R. Smith ORCID iD [aut, cre, cph], Emmanuel Paradis ORCID iD [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>
URL: https://ms609.github.io/TreeTools/, https://github.com/ms609/TreeTools/
NeedsCompilation: yes
SystemRequirements: C++11
Language: en-GB
Citation: TreeTools citation info
Materials: NEWS
CRAN checks: TreeTools results

Downloads:

Reference manual: TreeTools.pdf
Vignettes: Navigating the file system in R
Load phylogenetic data
Load phylogenetic trees
Package source: TreeTools_1.3.0.tar.gz
Windows binaries: r-devel: TreeTools_1.3.0.zip, r-release: TreeTools_1.3.0.zip, r-oldrel: TreeTools_1.2.0.zip
macOS binaries: r-release: TreeTools_1.3.0.tgz, r-oldrel: TreeTools_1.3.0.tgz
Old sources: TreeTools archive

Reverse dependencies:

Reverse imports: Quartet, TBRDist, TreeDist, TreeSearch

Linking:

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