> ## Documentation Index
> Fetch the complete documentation index at: https://docs.kalarislabs.com/llms.txt
> Use this file to discover all available pages before exploring further.

# etetoolkit — AI agent skill for life sciences

> Analyze, manipulate, compare, annotate, and visualize phylogenetic or other hierarchical trees with ETE 4.

# `etetoolkit`

> Analyze, manipulate, compare, annotate, and visualize phylogenetic or other hierarchical trees with ETE 4. Use for Newick/Nexus tree I/O, topology edits and pattern matching, Robinson-Foulds comparisons, gene-tree evolutionary events and reconciliation, NCBI/GTDB taxonomy, SmartView exploration, and publication rendering. Do not use it to infer trees from raw sequences; align sequences and infer a tree first.

**Category:** [life-sciences](/research-agent-skills/skills#life-sciences) · **License:** GPL-3.0-or-later · **Version:** 2.1

## Install

```bash theme={null}
npx research-agent-skills install etetoolkit
npx skills add KalarisLabs/research-agent-skills --skill etetoolkit
```

## When to use it

Analyze, manipulate, compare, annotate, and visualize phylogenetic or other hierarchical trees with ETE 4. Use for Newick/Nexus tree I/O, topology edits and pattern matching, Robinson-Foulds comparisons, gene-tree evolutionary events and reconciliation, NCBI/GTDB taxonomy, SmartView exploration, and publication rendering. Do not use it to infer trees from raw sequences; align sequences and infer a tree first.

## Full playbook

Read [SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/main/skills/etetoolkit/SKILL.md) for the complete workflow, references and any scripts. The agent installer copies the full skill folder.


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