domains / families / science / etetoolkit

etetoolkit

combined

Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics. Analyzes, manipulates, compares, annotates, and visualizes phylogenetic or other hierarchical trees with ETE 4. Supports Newick/Nexus tree I/O, topology edits and pattern matching, Robinson-Foulds comparisons, gene-tree evolutionary events and reconciliation, NCBI/GTDB taxonomy, SmartView exploration, and publication rendering. Applies to existing trees after alignment and phylogenetic inference, rather than inferring trees from raw sequences.

When to use

• Read Newick/Nexus, then inspect, annotate, transform, root, prune, and write
• Compare topologies and calculate phylogenetic distances
• Find repeated subtree topologies with `TreePattern`
• Analyze gene trees with `PhyloTree`
• Query local NCBI or GTDB taxonomy databases
• Explore large trees interactively with SmartView
• Render PNG with SmartView or PNG/PDF/SVG with the optional Qt treeview
• **Preprocess phylogenetic trees**: convert formats (Newick/NHX/PhyloXML), reroot (midpoint/outgroup), prune taxa, and resolve polytomies before downstream analyses.

Skill page

Conflict

The copies overlap on ETE tree I/O, pruning, rooting, Robinson-Foulds comparison, gene-tree event detection, NCBI taxonomy, and visualization, but they target different ETE generations and include material steps the others lack. K-Dense-AI/scientific-agent-skills is the only copy targeting ETE 4.4.0 with ete4-specific API constraints, installation extras, SmartView/static rendering, and a migration warning. foryourhealth111-pixel/Vibe-Skills and FreedomIntelligence/OpenClaw-Medical-Skills are nearly identical ETE 3 skills and add a bundled command-line tree_operations.py workflow. aipoch/medical-research-skills adds clustering/dendrogram support and detailed Newick format-code guidance. Crowning one copy would hide either the ETE 4 procedure or the ETE 3 command-line/clustering alternatives.