How do I install the Bioconductor Treeio skill?

Run npx skillmds@latest add biomate-ai/bioconductor-treeio in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Bioconductor Treeio safe to use?

This skill has not completed SkillMD's automated safety review yet. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Bioconductor Treeio?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Bioconductor Treeio free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Bioconductor Treeio?

biomate-ai (@biomate-ai) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Bioconductor Treeio by biomate-ai — Agent Skill

Name: Bioconductor Treeio
Author: biomate-ai

Bioconductor Treeio

'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

biomate-ai 4bc3063 3.4 KB Updated Sep 17, 2026

File contents

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

Run this on BioMate

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.

▶ Open treeio on BioMate →

---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---# 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---## Run this on BioMateThis 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](https://www.biomate.ai?ref=kb&pkg=treeio)** — free to start.▶ **[Open `treeio` on BioMate →](https://www.biomate.ai?ref=kb&pkg=treeio)**

Frequently asked questions