| name | bioconductor-treeio |
| description | '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 |
| when_to_use | Use when: Phylogenetic Tree Input and Output: Managing phylogenetic tree data using the package's core base classes.; Vignette Redirection: Accessing the full documentation and tutorials by navigating to the external treedata-book resource linked in the package stub.. Not for: Detailed In-Package Tutorials: For comprehensive workflows, use the external treedata-book website because the built-in vignette is only a stub.; Tree Reconstruction: For inferring phylogenetic trees from sequence alignments, use external tools becau |
| user-invocable | false |
treeio
Dependencies & Environment
Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
- Version: 1.36.1 · Bioconductor: 3.23 · R: ≥ 4.6
- Imports: ape, dplyr, jsonlite, magrittr, rlang, tibble, tidytree, yulab.utils
- Install:
BiocManager::install("treeio")
When to Use
- Phylogenetic Tree Input and Output: Managing phylogenetic tree data using the package's core base classes.
- Vignette Redirection: Accessing the full documentation and tutorials by navigating to the external
treedata-book resource linked in the package stub.
When NOT to Use
- Detailed In-Package Tutorials: For comprehensive workflows, use the external
treedata-book website because the built-in vignette is only a stub.
- Tree Reconstruction: For inferring phylogenetic trees from sequence alignments, use external tools because
treeio focuses strictly on base classes for input and output.
Data Requirements
- Tree Files: Phylogenetic tree files compatible with the package's base classes for input and output.
Key Parameters
- tidy (FALSE):
knitr::opts_chunk$set option used to control code formatting in the vignette.
- message (FALSE):
knitr::opts_chunk$set option used to suppress messages during document compilation.
Best Practices
- Consult External Documentation: Go to
https://yulab-smu.top/treedata-book/ for the full vignette and comprehensive workflow instructions.
- Clean Report Compilation: Set
tidy = FALSE and message = FALSE in knitr::opts_chunk$set when compiling reports to avoid clutter.
- Utilize Base Classes: Rely on the base classes provided by the package for consistent phylogenetic tree input and output.
Common Pitfalls
- Missing Documentation: Looking for detailed tutorials in the standard vignette fails because it is only a stub. Fix: Go to the external
treedata-book link provided in the vignette text.
- Unwanted Compilation Messages: R outputs verbose messages during document rendering. Fix: Use
message = FALSE in the knitr::opts_chunk$set options.
Alternatives
- ape: Provides basic phylogenetic tree structures, but
treeio offers specialized base classes for input and output.
- phylobase: Another package for tree classes, but
treeio is specifically designed for integration with the treedata-book ecosystem.
- tidytree: Works alongside
treeio for tidy data manipulation rather than just input/output.
Citations
- Guangchuang Yu (2026). "treeio: Base Classes and Functions for Phylogenetic Tree Input and Output".
References
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