'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
Start a fresh conversation. Replace the highlighted placeholders.
Use bioconductor-treeio to import and organize [phylogenetic tree files] with [associated external data], and provide an R-based input/output workflow; do not infer a new tree from sequence alignments.
Required inputs
[phylogenetic tree files]
[associated external data]
User-approved starter prompt based on a pinned source version; check current skill requirements before running. Task evidence ↗
SKILL.md
name: bioconductor-treeiodescription: "'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.
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".
This skill is the knowledge layer — when, why, and how to use treeio. To run this analysis on your own data with managed compute, automated QC, and reproducible outputs, use BioMate — free to start.