DOI: 10.18129/B9.bioc.treeio  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see treeio.

Base Classes and Functions for Phylogenetic Tree Input and Output

Bioconductor version: 3.17

'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>

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


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biocViews Alignment, Annotation, Clustering, DataImport, DataRepresentation, MultipleSequenceAlignment, Phylogenetics, Software
Version 1.24.3
In Bioconductor since BioC 3.5 (R-3.4) (6.5 years)
License Artistic-2.0
Depends R (>= 3.6.0)
Imports ape, dplyr, jsonlite, magrittr, methods, rlang, tibble, tidytree (>= 0.3.9), utils, cli
Suggests Biostrings, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, testthat, tidyr, vroom, xml2, yaml, purrr
Depends On Me
Imports Me, ggtree, MicrobiotaProcess, TreeSummarizedExperiment
Suggests Me enrichplot, ggtreeDendro, ggtreeExtra, rfaRm
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