---
title: "ETE Toolkit 4 - Air Market"
description: "Once you have a tree, there is a lot left to do: reshape it, annotate it, compare it with another one, and draw it well enough to publish. This handles that side of the work, including taxonomy looku…"
canonical: "https://airmarket.ai/app/etetoolkit"
---

[Air Market](/) / [Data & Analytics](/category/data) / ETE Toolkit 4

Skill by [K-Dense](/@k-dense-ai)

# ETE Toolkit 4

Work on a tree you already have, from edits to a publishable figure

## What this does

Once you have a tree, there is a lot left to do: reshape it, annotate it, compare it with another one, and draw it well enough to publish. This handles that side of the work, including taxonomy lookups and interactive exploration. It does not build trees from raw sequences - align and infer first, then come here.

### Top 3 things it does for you

- Read and write Newick or Nexus trees
- Edit a topology or search it for a pattern
- Compare two trees with Robinson-Foulds

## Information

**ETE Toolkit 4 at a glance**

|  |  |
| --- | --- |
| Kind | Skill |
| Publisher | [K-Dense](/@k-dense-ai) |
| Category | [Data & Analytics](/category/data) |
| Works with | Agent Skills - an open standard supported by 40+ agents |
| Version | 2.0 |
| Size | 101 KB |
| Licence | MIT |
| Repository | [k-dense-ai/scientific-agent-skills](https://github.com/k-dense-ai/scientific-agent-skills/tree/81e316bc89f7fda176b092d2bceb959204710b0a/skills/etetoolkit) |
| GitHub stars | 34,239 (as of Nov 2026) |

## Security report

**Verified.** AIR scanned this exact version of ETE Toolkit 4 and flagged nothing. AIR's verdict: **safe**.

**What ETE Toolkit 4's check was run against**

|  |  |
| --- | --- |
| Commit | 81e316bc89f7fda176b092d2bceb959204710b0a |
| Content hash | e53ba50aa5ae39bf92e659be3fb65d90e073e75a7a75997b7363132e9bbbe656 |
| Files read | [Browse the files at this exact commit](https://github.com/k-dense-ai/scientific-agent-skills/blob/81e316bc89f7fda176b092d2bceb959204710b0a/skills/etetoolkit/SKILL.md) |

A scan is named by the exact content it read, not by a version number. A different version is a different artifact, and nothing here applies to a version AIR has not scanned.

[Read the full security report for ETE Toolkit 4](/security/etetoolkit)

## About ETE Toolkit 4

This analyzes, manipulates, compares, annotates and visualizes phylogenetic and other hierarchical trees with ETE 4. It covers Newick and Nexus tree input and output, topology edits and pattern matching, Robinson-Foulds comparisons, gene-tree evolutionary events and reconciliation, NCBI and GTDB taxonomy, SmartView exploration, and publication rendering.

It is not for inferring trees from raw sequences. Align your sequences and infer a tree first, then bring the tree here.

## What's inside

- SKILL.md - instructions
- references/api_reference.md - reference
- references/migration-ete3-to-ete4.md - reference
- references/taxonomy.md - reference
- references/visualization.md - reference
- references/workflows.md - reference
- scripts/quick_visualize.py - script
- scripts/tree_operations.py - script

## Questions

### Is ETE Toolkit 4 safe to install?

AIR scanned this exact version of ETE Toolkit 4 and flagged nothing. AIR's verdict: safe. The verdict is named by the content that was read, at commit 81e316bc89f7, so it cannot drift onto a version nobody scanned. The full report is at https://airmarket.ai/security/etetoolkit.

### How do I install ETE Toolkit 4?

Open https://airmarket.ai/app/etetoolkit on Air Market and use the install action: Air Market hands Claude a prompt naming this exact skill, and Claude sets it up. Source, pinned to the exact commit this listing describes: https://github.com/k-dense-ai/scientific-agent-skills/tree/81e316bc89f7fda176b092d2bceb959204710b0a/skills/etetoolkit. Install from that link, not the branch.

## Related on Air Market

- [More Data & Analytics listings](/category/data)
- [Everything by K-Dense](/@k-dense-ai)

---

Canonical URL: <https://airmarket.ai/app/etetoolkit>