treeio

DOI: 10.18129/B9.bioc.treeio    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see treeio.

Base Classes and Functions for Phylogenetic Tree Input and Output

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

HTML	R Script	01 Importing trees with data
HTML	R Script	02 Exporting trees with data
PDF		Reference Manual

Details

biocViews	Alignment, Annotation, Clustering, DataImport, DataRepresentation, MultipleSequenceAlignment, Software
Version	1.6.2
In Bioconductor since	BioC 3.5 (R-3.4) (2 years)
License	Artistic-2.0
Depends	R (>= 3.4.0)
Imports	ape, dplyr, jsonlite, magrittr, methods, rlang, rvcheck, tibble, tidytree (>= 0.1.7), utils
LinkingTo
Suggests	ggplot2, ggtree, knitr, prettydoc, testthat, tidyr
SystemRequirements
Enhances
URL	https://guangchuangyu.github.io/software/treeio
BugReports	https://github.com/GuangchuangYu/treeio/issues
Depends On Me
Imports Me	ggtree
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	treeio_1.6.2.tar.gz
Windows Binary	treeio_1.6.2.zip
Mac OS X 10.11 (El Capitan)	treeio_1.6.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/treeio
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/treeio
Package Short Url	http://bioconductor.org/packages/treeio/
Package Downloads Report	Download Stats