bioconductor-treeio

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

• Homepage: bioconductor.org/packages/treeio
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/treeio/inst/doc/treeio.html

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