https://github.com/ms609/treetools

Create, modify and analyse phylogenetic trees in R
https://github.com/ms609/treetools

cran evolutionary-biology phylogenetic-trees phylogenetics r-package

Last synced: about 1 month ago
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Create, modify and analyse phylogenetic trees in R

• Host: GitHub
• URL: https://github.com/ms609/treetools
• Owner: ms609
• Created: 2019-10-18T08:02:40.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2025-05-05T11:17:04.000Z (about 1 month ago)
• Last Synced: 2025-05-08T23:43:24.983Z (about 1 month ago)
• Topics: cran, evolutionary-biology, phylogenetic-trees, phylogenetics, r-package
• Language: R
• Homepage: https://ms609.github.io/TreeTools/
• Size: 18.5 MB
• Stars: 23
• Watchers: 3
• Forks: 7
• Open Issues: 16
• Metadata Files:
  • Readme: README.md
  • Changelog: NEWS.md
  • Contributing: CONTRIBUTING.md
  • Code of conduct: CODE_OF_CONDUCT.md
  • Codemeta: codemeta.json

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README

        
# TreeTools

[![codecov](https://codecov.io/gh/ms609/TreeTools/branch/master/graph/badge.svg)](https://codecov.io/gh/ms609/TreeTools)

[![CRAN Status Badge](https://www.r-pkg.org/badges/version/TreeTools)](https://cran.r-project.org/package=TreeTools)

[![CRAN Downloads](https://cranlogs.r-pkg.org/badges/TreeTools)](https://ms609.github.io/usage/#treetools)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3522726.svg)](https://doi.org/10.5281/zenodo.3522725)

[![Project Status: Active – – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)

'TreeTools' is an R package that provides 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 and 

[TNT](https://www.lillo.org.ar/phylogeny/tnt/) formats;

and analysis of partitions and cladistic information.

It complements packages such as 

['ape'](https://cran.r-project.org/package=ape),

['phangorn'](https://cran.r-project.org/package=phangorn) and

['phytools'](https://cran.r-project.org/package=phytools),

aiming for efficient and robust implementations of functions, typically

applied to unweighted trees (i.e. those without edge lengths).

# Installation

Install and load the library from CRAN as follows:

```r

install.packages("TreeTools")

library("TreeTools")

```

Install the very latest version, which may be under development, with:

```r

if (!require("devtools")) install.packages("devtools")

devtools::install_github("ms609/TreeTools")

```

Please note that the 'TreeTools' project is released with a

[Contributor Code of Conduct](CODE_OF_CONDUCT.md).

By contributing to this project, you agree to abide by its terms.