alterlab-etetoolkit

# 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. ## When to Use - Parsing, traversing, or reformatting tree files (Newick / NHX / PhyloXML / NeXML) - Pruning, rooting, collapsing, or resolving polytomies in a tree - Detecting duplication/speciation events and inferring orthologs/paralogs from gene trees - Querying NCBI Taxonomy (taxid/name translation, lineages, taxonomy trees) - Producing publication-quality PDF/SVG/PNG tree figures - Comparing trees (Robinson-Foulds) or analyzing clustering dendrograms ## Core Capabilities ETE exposes six capability areas. Each has detailed, copy-ready code in the references (see Index below). 1. **Tree manipulation** — I/O across formats, traversal (pre/post/levelorder), topology edits (prune, root, collapse), distances, RF tree comparison. 2. **Phylogenetic analysis** — alignment linkage, species naming, duplication/speciation detection (Species Overlap or reconciliation), orthology/paralogy. 3. **NCBI Taxonomy** — local cached DB, taxid↔name translation, lineage retrieval, taxonomy-tree building, tree annotation. 4. **Visualization** — PNG/PDF/SVG export, rectangular/circular layouts, `NodeStyle`, `Face` objects, layout functions, interactive GUI. 5. **Clustering analysis** — `Clust...