treeio

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see treeio.

Base Classes and Functions for Phylogenetic Tree Input and Output


Bioconductor version: 3.9

Base classes and functions for parsing and exporting phylogenetic trees. 'treeio' supports parsing analysis findings from commonly used software packages, allows linking external data to phylogeny and merging tree data obtained from different sources. It also supports exporting phylogenetic tree with heterogeneous associated data to a single tree file.

Author: Guangchuang Yu [aut, cre] , Tommy Tsan-Yuk Lam [ctb, ths], Casey Dunn [ctb], Bradley Jones [ctb], Tyler Bradley [ctb]

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

Citation (from within R, enter citation("treeio")):

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("treeio")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("treeio")
treeio HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Alignment, Annotation, Clustering, DataImport, DataRepresentation, MultipleSequenceAlignment, Software
Version 1.8.2
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License Artistic-2.0
Depends R (>= 3.4.0)
Imports ape, dplyr, jsonlite, magrittr, methods, rlang, tibble, tidytree (>= 0.2.3), utils
System Requirements
URL https://guangchuangyu.github.io/software/treeio
Bug Reports https://github.com/GuangchuangYu/treeio/issues
See More
Suggests Biostrings, ggplot2, ggtree, knitr, phangorn, prettydoc, testthat, tidyr
Linking To
Enhances
Depends On Me
Imports Me ggtree
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package treeio_1.8.2.tar.gz
Windows Binary treeio_1.8.2.zip
Mac OS X 10.11 (El Capitan) treeio_1.8.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/treeio
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/treeio
Bioc Package Browser https://code.bioconductor.org/browse/treeio/
Package Short Url https://bioconductor.org/packages/treeio/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive