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>
citation("treeio")):
Installation
To install this package, start R (version "3.5") 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")| 01 Importing trees with data | HTML | R Script |
| 02 Exporting trees with data | HTML | R Script |
| Reference Manual |
Details
| biocViews | Alignment, Annotation, Clustering, DataImport, DataRepresentation, MultipleSequenceAlignment, Software |
| Version | 1.6.2 |
| 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, rvcheck, tibble, tidytree (>= 0.1.7), utils |
| System Requirements | |
| URL | https://guangchuangyu.github.io/software/treeio |
| Bug Reports | https://github.com/GuangchuangYu/treeio/issues |
See More
| Suggests | ggplot2, ggtree, knitr, 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_1.6.2.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 |
| 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 3.8 | Source Archive |