etetoolkit

Topics in the source

• ETE Toolkit Skill
• Overview
• Core Capabilities
• 1. Tree Manipulation and Analysis
• 2. Phylogenetic Analysis
• 3. NCBI Taxonomy Integration
• 4. Tree Visualization
• 5. Clustering Analysis

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. 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: 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 e

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