treeio

DOI: 10.18129/B9.bioc.treeio    

This is the development version of treeio; for the stable release version, see treeio.

Base Classes and Functions for Phylogenetic Tree Input and Output

Bioconductor version: Development (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] (<https://orcid.org/0000-0002-6485-8781>), 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 and enter:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("treeio", version = "devel")

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 1.5.3
In Bioconductor since BioC 3.5 (R-3.4) (1.5 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
Build Report  

Package Archives

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

Source Package treeio_1.5.3.tar.gz
Windows Binary treeio_1.5.3.zip
Mac OS X 10.11 (El Capitan) treeio_1.5.3.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: