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; 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 partitions and partition information.

Version: 0.1.3
Depends: R (≥ 3.4.0), ape (≥ 5.0)
Imports: colorspace, phangorn (≥ 2.2.1), R.cache
LinkingTo: Rcpp
Suggests: knitr, Rcpp, Rdpack, rmarkdown, shiny, testthat
Published: 2019-12-19
Author: Martin R. Smith ORCID iD [aut, cre, cph], Emmanuel Paradis ORCID iD [cph], Klaus Schliep 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; phangorn by Klaus Scheip <doi:10.1093/bioinformatics/btq706>
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_0.1.3.tar.gz
Windows binaries: r-devel: TreeTools_0.1.3.zip, r-devel-gcc8: TreeTools_0.1.3.zip, r-release: TreeTools_0.1.3.zip, r-oldrel: TreeTools_0.1.3.zip
OS X binaries: r-release: TreeTools_0.1.3.tgz, r-oldrel: TreeTools_0.1.3.tgz
Old sources: TreeTools archive

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