treeio
Base Classes and Functions for Phylogenetic Tree Input and Output
Bioconductor version: Release (3.19)
'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("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 | ||
| NEWS | Text |
Details
| biocViews | Alignment, Annotation, Clustering, DataImport, DataRepresentation, MultipleSequenceAlignment, Phylogenetics, Software |
| Version | 1.28.0 |
| 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 (> 0.1.1) |
| System Requirements | |
| URL | https://github.com/YuLab-SMU/treeio(devel) https://docs.ropensci.org/treeio/(docs) https://www.amazon.com/Integration-Manipulation-Visualization-Phylogenetic-Computational-ebook/dp/B0B5NLZR1Z/(book) https://doi.org/10.1093/molbev/msz240(paper) |
| Bug Reports | https://github.com/YuLab-SMU/treeio/issues |
See More
| Suggests | Biostrings, cli, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, purrr, testthat, tidyr, vroom, xml2, yaml |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | MicrobiotaProcess, TreeSummarizedExperiment, ggtree, 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_1.28.0.tar.gz |
| Windows Binary (x86_64) | treeio_1.28.0.zip |
| macOS Binary (x86_64) | treeio_1.28.0.tgz |
| macOS Binary (arm64) | treeio_1.28.0.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 |