treeio

Base Classes and Functions for Phylogenetic Tree Input and Output

Bioconductor version: Release (3.20)

'treeio' is an R package to make it easier to import and store phylogenetic tree with associated data; and to link external data from different sources to phylogeny. It also supports exporting phylogenetic tree with heterogeneous associated data to a single tree file and can be served as a platform for merging tree with associated data and converting file formats.

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

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

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

Installation

To install this package, start R (version "4.4") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, Annotation, Clustering, DataImport, DataRepresentation, MultipleSequenceAlignment, Phylogenetics, Software
Version	1.30.0
In Bioconductor since	BioC 3.5 (R-3.4) (7.5 years)
License	Artistic-2.0
Depends	R (>= 3.6.0)
Imports	ape, dplyr, jsonlite, magrittr, methods, rlang, stats, tibble, tidytree (>= 0.4.5), utils, yulab.utils (>= 0.1.6)
System Requirements
URL	https://yulab-smu.top/contribution-tree-data/
Bug Reports	https://github.com/YuLab-SMU/treeio/issues

Suggests	Biostrings, cli, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, purrr, testthat, tidyr, vroom, xml2, yaml
Linking To
Enhances
Depends On Me
Imports Me	ggtree, MicrobiotaProcess, TreeSummarizedExperiment, geneplast.data, EvoPhylo, RevGadgets, shinyTempSignal
Suggests Me	ggtreeDendro, ggtreeExtra, rfaRm, FossilSim, idiogramFISH, MetaNet, nosoi
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	treeio_1.30.0.tar.gz
Windows Binary (x86_64)	treeio_1.30.0.zip
macOS Binary (x86_64)	treeio_1.30.0.tgz
macOS Binary (arm64)	treeio_1.30.0.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