etetoolkit

Files (9)

• SKILL.md
• api_reference.md · references/
• migration-ete3-to-ete4.md · references/
• review.md · references/
• taxonomy.md · references/
• visualization.md · references/
• workflows.md · references/
• quick_visualize.py · scripts/
• tree_operations.py · scripts/

SKILL.md (first lines)

# 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"
```

Add only the visualization extra required by the workflow:

```bash
# SmartView static PNG screenshots
uv pip install "ete4[render-sm]==4.4.0"

# Legacy Qt renderer for PNG, PDF, and SVG
uv pip install "ete4[treeview]==4.4.0"
```

Confirm the active environment:

```bash
uv run --no-project --isolated --with "ete4==4.4.0" python -c "import ete4; print(ete4.__version__)"
```

No credentials are required. NCBI and GTDB workflows download public taxonomy
data and can consume substantial disk space; see
[`references/taxonomy.md`](references/taxonomy.md) before the first update.

## Quick Start

```python
from pathlib import Path

from ete4 import Tree

# Use an open file object for files; reserve strings for Newick text.
with Path("tree.nw").open(encoding="utf-8") as handle:
    tree = Tree(handle, parser=1)  # parser 1: internal node names

print(tree.to_str(props=["name", "dist"], compact=True))
print("Leaves:", list(tree.leaf_names()))

# Search and annotate.
focal = tree["species1"]
focal.add_props(host="human", status="focal")

# Keep selected tips while preserving pairwise branch-length distances.
tree.prune(
    ["species1", "species2", "species3"],
    preserve_branch_length=True,
)

# Root and serialize explicitly.
tree.set_midpoint_outgroup()
tree.write(
    outfile="processed.nw",
    parser=1,
    props=["host", "status"],
)
```

Choose the parser deliberately. A parser mismatch is the most common cause of
`NewickError`, lost internal labels, or support values being read as names.
See [`references/api_reference.md`](references/api_reference.md).

## Core Workflows

### Inspect and transform a tree

```python
from ete4 import Tree

tree = Tree("((A:1,B:1)CladeAB:0.4,C:2)Root;", parser=1)

From K-Dense-AI/scientific-agent-skills, GPL-3.0.

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