Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
---
name: etetoolkit
description: Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
license: GPL-3.0 license
metadata: {"version": "1.0", "skill-author": "K-Dense Inc."}
---
# 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
… load the full skill through Skill Me