etetoolkit - Phylogenetic Tree Analysis with ETE
Manipulates, analyzes, compares, visualizes, and annotates phylogenetic and hierarchical trees for phylogenomics and clustering.
Tags
Updated: 2026-10-03Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Read and write tree formats
- Traverse hierarchical trees
- Modify tree topology
- Calculate tree distances
- Detect evolutionary events
- Identify orthologs and paralogs
- Integrate NCBI taxonomy
- Render styled tree visualizations
- Analyze clustering results
- Compare tree topologies
Inputs
- Phylogenetic tree files
- Sequence alignment files
- Taxon names or IDs
- Gene naming rules
- Clustering data matrices
- Visualization settings
- Output file paths
Outputs
- Modified tree files
- Tree statistics
- Evolutionary event results
- Ortholog group files
- Taxonomy-annotated trees
- Rendered PNG, PDF, or SVG files
- Cluster quality metrics
- Tree comparison results
- Heatmap visualizations
Requirements
- Python environment with ETE
- NCBI taxonomy access when needed