Agent skill · research science · aiskillstore
etetoolkit
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
Why this skill is useful
Adds specific commands and workflows for phylogenetic tree manipulation and evolutionary event detection that the AI wouldn't reliably generate on its own.
What it needs
Requires ete3 installed locally. About 9k tokens when loaded. Last updated 2026-08-07. 405 stars on the source repository.
What this skill does
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: Use scripts/treeoperations.py for command-line tree manipulation: 2. Phylogenetic Analysis Analyze gene trees with evolutionary event detection: Sequence alignment integration: Link trees to multiple sequence alignments (FASTA, Phylip) Species naming: Automatic or custom species extraction from gene names Evolutionary events: Detect duplication and speciation events using Species Overlap or tree reconciliation Orthology detection: Identify orthologs and paralogs based on evolutionary events Gene family analysis: Split trees by duplications, collapse lineage-specific expansions Workflow for gene tree analysis: Finding orthologs and paralogs: 3. NCBI Taxonomy Integration Integrate taxonomic information from NCBI Taxonomy database: Database access: Automatic download and local caching of NCBI taxonomy (~300MB) Taxid/name translation: Convert between taxonomic IDs and scientific names Lineage retrieval: Get complete evolutionary lineages Taxonomy trees: Build species trees connecting specified taxa Tree annotation: Automatically annotate trees with taxonomic information Building taxonomy-based trees: Annotating existing trees: 4. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills aiskillstore/etetoolkit--f6651f