What tree formats does the ETE Toolkit support?

ETE supports common phylogenetic formats including Newick, NHX, PhyloXML, and NeXML, allowing for seamless reading, writing, and conversion of hierarchical data.

Does it require a local database for NCBI taxonomy integration?

Upon first use, the NCBITaxa module automatically downloads and caches a local SQLite version of the NCBI taxonomy database (approx. 300MB) to enable high-speed taxonomic lookups.

Can I use this skill to identify orthologs and paralogs?

Yes, the skill includes specialized logic for detecting speciation and duplication events through tree reconciliation, which is essential for identifying orthologs and paralogs within gene trees.

Can I generate high-resolution images of my trees?

Absolutely. The skill supports rendering trees in PNG, PDF, and SVG formats with highly customizable styles, node faces, and both rectangular or circular layout modes.

ETE Toolkit Phylogenetic Analysis

Name: ETE Toolkit Phylogenetic Analysis
Author: pur3v4d3r

bypur3v4d3r

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Data Science & ML

Manipulates, analyzes, and visualizes phylogenetic trees with advanced support for evolutionary event detection and NCBI taxonomy integration.

About

The ETE Toolkit skill empowers Claude to perform complex phylogenetic and phylogenomic tasks using the Environment for Tree Exploration (ETE). It provides specialized capabilities for loading various tree formats (Newick, NHX), performing topological manipulations, detecting duplication and speciation events, and automating NCBI taxonomy lookups. Whether you are conducting gene family analysis, calculating Robinson-Foulds distances, or generating publication-quality tree visualizations in SVG or PDF, this skill streamlines the entire evolutionary biology workflow within your development environment.

Key Features

Comprehensive tree manipulation including pruning, rooting, and format conversion (Newick, NHX, PhyloXML)
Publication-quality tree visualization with customizable layouts (rectangular, circular) and graphical annotations
Automated NCBI Taxonomy integration for species naming, lineage retrieval, and taxonomic tree construction
1 GitHub stars
Evolutionary event detection to identify orthologs and paralogs via tree reconciliation and species overlap
Hierarchical clustering analysis (ClusterTree) with data matrix linking and cluster validation metrics

Use Cases

Comparing multiple tree topologies using Robinson-Foulds distance calculations and bipartition analysis
Annotating phylogenetic trees with taxonomic metadata and rendering them for scientific research publications
Automating phylogenomic pipelines from raw gene tree input to final ortholog group identification

About

Key Features

Comprehensive tree manipulation including pruning, rooting, and format conversion (Newick, NHX, PhyloXML)
Publication-quality tree visualization with customizable layouts (rectangular, circular) and graphical annotations
Automated NCBI Taxonomy integration for species naming, lineage retrieval, and taxonomic tree construction
1 GitHub stars
Evolutionary event detection to identify orthologs and paralogs via tree reconciliation and species overlap
Hierarchical clustering analysis (ClusterTree) with data matrix linking and cluster validation metrics

Use Cases

Comparing multiple tree topologies using Robinson-Foulds distance calculations and bipartition analysis
Annotating phylogenetic trees with taxonomic metadata and rendering them for scientific research publications
Automating phylogenomic pipelines from raw gene tree input to final ortholog group identification