# Etetoolkit

Analyzes, manipulates, compares, annotates, and visualizes phylogenetic or other...

- Repository: https://github.com/K-Dense-AI/scientific-agent-skills (55651 stars)
- Category: Engineering
- License: GPL-3.0-or-later
- Last updated: 2026-10-26
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add K-Dense-AI/scientific-agent-skills --skill etetoolkit -g -a claude-code -y`
Codex: `npx skills add K-Dense-AI/scientific-agent-skills --skill etetoolkit -g -a codex -y`
Cursor: `npx skills add K-Dense-AI/scientific-agent-skills --skill etetoolkit -g -a cursor -y`
Gemini CLI: `npx skills add K-Dense-AI/scientific-agent-skills --skill etetoolkit -g -a gemini-cli -y`

## Description

Analyzes, manipulates, compares, annotates, and visualizes phylogenetic or other hierarchical trees with ETE 4. Supports 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. Applies to existing trees after alignment and phylogenetic inference, rather than inferring trees from raw sequences.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# ETE Toolkit 4

## Scope

Use ETE 4 to work with an existing tree:

- Read Newick/Nexus, then inspect, annotate, transform, root, prune, and write
  Newick trees
- Compare topologies and calculate phylogenetic distances
- Find repeated subtree topologies with `TreePattern`
- Analyze gene trees with `PhyloTree`
- Query local NCBI or GTDB taxonomy databases
- Explore large trees interactively with SmartView
- Render PNG with SmartView or PNG/PDF/SVG with the optional Qt treeview

ETE does not replace sequence alignment or phylogenetic inference software. For
raw sequences, first use MAFFT or another aligner and IQ-TREE 2, FastTree, or
another inference tool; then load the resulting tree into ETE.

## Current Target

This skill targets **ETE 4.4.0**, released September 3, 2025 and verified as the
current PyPI release on September 30, 2026.
Core, phylogeny, local synthetic taxonomy and helper checks target this released
package, not unreleased upstream changes. See
[`references/review.md`](references/review.md) for executed coverage and limitations.

Use `https://etetoolkit.github.io/ete/` for ETE 4 documentation. The
`etetoolkit.org/docs/latest` pages are legacy ETE 3 documentation despite the
URL name.

Do not silently translate these examples back to ETE 3:

- Package and import: `ete4`, not `ete3`
- File input: pass an open file object; use strings for Newick text and do not
  rely on path-string heuristics retained in ETE 4.4.0
- Newick selection: `parser=`, not `format=`
- Node metadata: `props`, `add_prop()`, and `add_props()`
- Iteration: `leaves()`, `descendants()`, and related methods return iterators
- Predicates: `node.is_leaf` and `node.is_root` are properties, not methods
- Node lookup: `tree["name"]`, not `tree & "name"`

For porting older code, load
[`references/migration-ete3-to-ete4.md`](references/migration-ete3-to-ete4.md).

## Installation

Install the pinned base package:

```bash
uv pip install "ete4==4.4.0"
```

The rest: https://github.com/K-Dense-AI/scientific-agent-skills/blob/HEAD/skills/etetoolkit/SKILL.md