Etetoolkit

If you're doing phylogenetics or working with evolutionary trees, this wraps the ETE3 toolkit for tree manipulation and analysis. You get Newick/NHX parsing, tree traversal and pruning, orthology detection through evolutionary event analysis, and NCBI taxonomy integration that auto-downloads the database locally. The visualization pipeline outputs publication-ready PDFs and SVGs with custom node styling and annotation faces. It includes helper scripts for quick operations like midpoint rooting and format conversion. The real value is in gene family analysis where you can detect duplication events, split trees into ortholog groups, and link trees to sequence alignments. Beats writing custom tree parsers when you need to do serious phylogenomic work beyond what basic Newick libraries offer.

skills.sh installs: 212
GitHub stars: 33.2K
last updated: Aug 21, 2026

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Install

$ npx -y skills add davila7/claude-code-templates --skill etetoolkit --agent claude-code

Installs into .claude/skills of the current project.

Files

ETE Toolkit Skill

Overview

ETE (Environment for Tree Exploration) is a toolkit for phylogenetic and hierarchical tree analysis. Manipulate trees, analyze evolutionary events, visualize results, and integrate with biological databases for phylogenomic research and clustering analysis.

Core Capabilities

1. Tree Manipulation and Analysis

Load, manipulate, and analyze hierarchical tree structures with support for:

Tree I/O: Read and write Newick, NHX, PhyloXML, and NeXML formats
Tree traversal: Navigate trees using preorder, postorder, or levelorder strategies
Topology modification: Prune, root, collapse nodes, resolve polytomies
Distance calculations: Compute branch lengths and topological distances between nodes
Tree comparison: Calculate Robinson-Foulds distances and identify topological differences

Common patterns:

from ete3 import Tree

# Load tree from file
tree = Tree("tree.nw", format=1)

# Basic statistics
print(f"Leaves: {len(tree)}")
print(f"Total nodes: {len(list(tree.traverse()))}")

SKILL.md on GitHub