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treeio

Base Classes and Functions for Phylogenetic Tree Input and Output

Bioconductor version: 3.23 · Package version: 1.36.1

'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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("treeio")

Details

MaintainerGuangchuang Yu <guangchuangyu@gmail.com>
AuthorGuangchuang Yu [aut, cre] (ORCID: <https://orcid.org/0000-0002-6485-8781>), Tommy Tsan-Yuk Lam [ctb, ths], Shuangbin Xu [ctb] (ORCID: <https://orcid.org/0000-0003-3513-5362>), Bradley Jones [ctb], Casey Dunn [ctb], Tyler Bradley [ctb], Konstantinos Geles [ctb]
LicenseArtistic-2.0
URLhttps://yulab-smu.top/contribution-tree-data/
Bug Reportshttps://github.com/YuLab-SMU/treeio/issues
Downloads rank29900
Source branchRELEASE_3_23
biocViewsAlignment, Annotation, Clustering, DataImport, DataRepresentation, MultipleSequenceAlignment, Phylogenetics, Software

Documentation

Download

Dependencies

Depends: R (>= 4.1.0)

Imports: ape, dplyr, jsonlite, magrittr, methods, rlang, stats, tibble, tidytree (>= 0.4.5), utils, yulab.utils (>= 0.1.6)

Suggests: Biostrings, cli, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, purrr, testthat, tidyr, vroom, xml2, yaml

Reverse dependencies

Imports Me (11): BioVizSeq, dowser, EvoPhylo, geneplast.data, ggtree, lefser, MicrobiotaProcess, RevGadgets, RPesto, shinyTempSignal, TreeSummarizedExperiment

Suggests Me (8): FossilSim, ggtreeDendro, ggtreeExtra, idiogramFISH, MetaNet, nosoi, rfaRm, treestructure