etetoolkit - Phylogenetic tree analysis with ETE
Manipulates and analyzes phylogenetic trees, detects evolutionary events, integrates NCBI taxonomy, visualizes trees, and evaluates clustering results.
Tags
Updated: 2026-10-03Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Parse phylogenetic tree formats
- Traverse hierarchical trees
- Modify tree topology
- Calculate tree distances
- Compare tree topologies
- Detect evolutionary events
- Identify orthologs and paralogs
- Integrate sequence alignments
- Query NCBI taxonomy
- Build taxonomy trees
- Annotate tree nodes
- Render tree visualizations
- Analyze clustering results
- Display heatmaps
Inputs
- Phylogenetic tree files
- Sequence alignment files
- Species names
- Gene names
- NCBI taxonomy data
- Clustering data matrices
- Output file paths
Outputs
- Modified tree files
- Evolutionary event classifications
- Ortholog and paralog groups
- Taxonomy-annotated trees
- Rendered tree images
- Clustering metrics
- Tree comparison metrics
- Heatmap visualizations
Requirements
- ETE toolkit installation
- NCBI taxonomy database access for taxonomy integration