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This is the development version of treeio; for the stable release version, see treeio.

Base Classes and Functions for Phylogenetic Tree Input and Output

Bioconductor version: Development (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>

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


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

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

treeio HTML R Script
Reference Manual PDF


biocViews Alignment, Annotation, Clustering, DataImport, DataRepresentation, MultipleSequenceAlignment, Phylogenetics, Software
Version 1.29.0
In Bioconductor since BioC 3.5 (R-3.4) (7 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
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Suggests Biostrings, cli, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, purrr, testthat, tidyr, vroom, xml2, yaml
Linking To
Depends On Me
Imports Me ggtree, MicrobiotaProcess, TreeSummarizedExperiment,, EvoPhylo, RevGadgets, shinyTempSignal
Suggests Me ggtreeDendro, ggtreeExtra, rfaRm, idiogramFISH, MetaNet, nosoi
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package treeio_1.29.0.tar.gz
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macOS Binary (x86_64) treeio_1.29.0.tgz
macOS Binary (arm64) treeio_1.29.0.tgz
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Source Repository (Developer Access) git clone
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