etetoolkit - Phylogenetic tree analysis with ETE
Manipulate, analyze, compare, annotate, visualize, and cluster phylogenetic and hierarchical trees with ETE.
Tags
Updated: 2026-10-03phylogeneticstree analysisevolutionary eventsorthologyNCBI taxonomytree visualizationhierarchical clustering
Capabilities
What this skill does
- Read and write 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
- Visualize data heatmaps
Inputs
- Phylogenetic tree files
- Sequence alignment files
- Taxon names
- Gene names
- Clustering data matrices
- Tree comparison files
- Visualization settings
Outputs
- Modified tree files
- Evolutionary event results
- Ortholog and paralog groups
- Taxonomy annotations
- Rendered PDF files
- Rendered SVG files
- Rendered PNG files
- Tree comparison metrics
- Clustering metrics
- Heatmap visualizations
Requirements
- Python environment
- ETE toolkit
- NCBI taxonomy database access
- Local taxonomy cache