Which tree formats are supported by ETE Toolkit?

It supports a wide range of formats including Newick, NHX, PhyloXML, and NeXML for both reading and writing operations.

Can this skill identify orthologs and paralogs?

Yes, it uses evolutionary event detection (speciation and duplication) to accurately identify orthology and paralogy relationships within gene trees.

Does it support hierarchical clustering data?

Yes, it includes a specialized ClusterTree class that connects trees to numerical data matrices, allowing for cluster validation and heatmap visualizations.

Can I generate figures for scientific publications?

Absolutely. The toolkit provides advanced rendering capabilities for circular or rectangular layouts in vector formats like PDF and SVG, as well as high-resolution PNGs.

How does the NCBI Taxonomy integration work?

Upon first use, the skill automatically downloads and caches a local copy of the NCBI taxonomy database (~300MB) to facilitate fast lookups, lineage retrieval, and tree annotation.

Phylogenetic Tree Analysis (ETE)

Name: Phylogenetic Tree Analysis (ETE)
Author: ricable

byricable

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データサイエンスとML

Manipulates, analyzes, and visualizes phylogenetic and hierarchical tree structures with biological database integration.

概要

ETE (Environment for Tree Exploration) is a comprehensive toolkit designed for the automated manipulation, analysis, and visualization of phylogenetic trees. It enables researchers to handle complex tree formats like Newick and NHX, detect evolutionary events such as orthology and paralogy, and integrate directly with the NCBI Taxonomy database for automated annotation. This skill is essential for phylogenomic research, providing the programmatic tools to perform topology modifications, compute tree distances, and generate publication-ready graphics in PDF, SVG, or PNG formats.

主な機能

Publication-Quality Visualization (PDF/SVG/PNG)
Hierarchical Clustering and Heatmap Analysis
1 GitHub stars
Evolutionary Event Detection (Orthology/Paralogy)
Comprehensive Tree I/O and Topology Manipulation
Deep NCBI Taxonomy Database Integration

ユースケース

Automating phylogenomic pipelines for gene family and evolutionary analysis
Comparing tree topologies and calculating Robinson-Foulds distances between models
Annotating phylogenetic trees with official NCBI taxonomic classifications and lineages

概要

主な機能

Publication-Quality Visualization (PDF/SVG/PNG)
Hierarchical Clustering and Heatmap Analysis
1 GitHub stars
Evolutionary Event Detection (Orthology/Paralogy)
Comprehensive Tree I/O and Topology Manipulation
Deep NCBI Taxonomy Database Integration

ユースケース

Automating phylogenomic pipelines for gene family and evolutionary analysis
Comparing tree topologies and calculating Robinson-Foulds distances between models
Annotating phylogenetic trees with official NCBI taxonomic classifications and lineages