etetoolkit
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
npx skills add LeonChaoX/qinyan-academic-skills --skill etetoolkit --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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:** ```python 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()))}") # Prune to taxa of interest taxa_to_keep = ["species1", "species2", "species3"] tree.prune(taxa_to_keep, preserve_branch_length=True) # Mid
- Overview
- Core Capabilities
- 1. Tree Manipulation and Analysis
- 2. Phylogenetic Analysis
- 3. NCBI Taxonomy Integration
- 4. Tree Visualization
- 5. Clustering Analysis
- 6. Tree Comparison
- Installation and Setup
- Common Use Cases
- Use Case 1: Phylogenomic Pipeline
- Use Case 2: Tree Preprocessing and Formatting
- Use Case 3: Publication-Quality Figures
- Use Case 4: Automated Tree Analysis
Display tree statistics python scripts/tree_operations.py stats tree.nw Convert format python scripts/tree_operations.py convert tree.nw output.nw --in-format 0 --out-format 1 Reroot tree python scripts/tree_operations.py reroot tree.nw rooted.nw --midpoint Prune to specific taxa python scripts/tree_operations.py prune tree.nw pruned.nw --keep-taxa "sp1,sp2,sp3" Show ASCII visualization python scripts/tree_operations.py ascii tree.nw
What does the etetoolkit skill do?
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
How do I install it?
Run `npx skills add LeonChaoX/qinyan-academic-skills --skill etetoolkit --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From LeonChaoX/qinyan-academic-skills, a repository with 759 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.