DOI: 10.18129/B9.bioc.treeio    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see treeio.

Base Classes and Functions for Phylogenetic Tree Input and Output

Bioconductor version: 3.8

Base classes and functions for parsing and exporting phylogenetic trees. 'treeio' supports parsing analysis findings from commonly used software packages, allows linking external data to phylogeny and merging tree data obtained from different sources. It also supports exporting phylogenetic tree with heterogeneous associated data to a single tree file.

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

Maintainer: Guangchuang Yu <guangchuangyu at>

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


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HTML R Script 01 Importing trees with data
HTML R Script 02 Exporting trees with data
PDF   Reference Manual


biocViews Alignment, Annotation, Clustering, DataImport, DataRepresentation, MultipleSequenceAlignment, Software
Version 1.6.2
In Bioconductor since BioC 3.5 (R-3.4) (2 years)
License Artistic-2.0
Depends R (>= 3.4.0)
Imports ape, dplyr, jsonlite, magrittr, methods, rlang, rvcheck, tibble, tidytree (>= 0.1.7), utils
Suggests ggplot2, ggtree, knitr, prettydoc, testthat, tidyr
Depends On Me
Imports Me ggtree
Suggests Me
Links To Me
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