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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: | 1.12.0 |
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: | 2024-07-25 |
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 |
Reference manual: | TreeTools.pdf |
Vignettes: |
File system navigation in R Loading phylogenetic data into R Loading phylogenetic trees into R |
Package source: | TreeTools_1.12.0.tar.gz |
Windows binaries: | r-devel: TreeTools_1.12.0.zip, r-release: TreeTools_1.12.0.zip, r-oldrel: TreeTools_1.12.0.zip |
macOS binaries: | r-release (arm64): TreeTools_1.12.0.tgz, r-oldrel (arm64): TreeTools_1.12.0.tgz, r-release (x86_64): TreeTools_1.12.0.tgz, r-oldrel (x86_64): TreeTools_1.12.0.tgz |
Old sources: | TreeTools archive |
Reverse depends: | Quartet |
Reverse imports: | avotrex, orthGS, Rogue, TBRDist, TotalCopheneticIndex, TreeDist, TreeSearch |
Reverse linking to: | TreeDist, TreeSearch |
Reverse suggests: | orthogene, phylosem |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.