Manipulate, analyze, and visualize phylogenetic trees in Python using ete3.
npx skills add https://github.com/rubensliv/k-dense-ai --skill etetoolkit-rubensliv
Please help me install this Agent Skill. Skill: etetoolkit Source: https://github.com/rubensliv/k-dense-ai/tree/main/scientific-skills/etetoolkit Command: npx skills add https://github.com/rubensliv/k-dense-ai --skill etetoolkit-rubensliv
ETE Toolkit enables researchers to manipulate, analyze, and visualize phylogenetic trees, integrate with taxonomic databases, and support phylogenomic workflows, bringing clarity to evolutionary analyses.
Load a gene tree with an alignment, set a species naming function, and render a publication-ready tree.
High-intent search queries and answers about installing and using this skill.
To annotate phylogenetic trees with NCBI taxonomy, you can integrate NCBITaxa to build and annotate topology trees, mapping species names to taxonomic ranks directly within your phylogenomic workflow.
Yes, you can compare gene trees and species trees by reading, pruning, and rerooting phylogenetic trees to perform topology comparisons across multiple gene families in your phylogenomic workflow.
Supported phylogenetic tree formats include Newick, NHX, PhyloXML, and NeXML, allowing you to load and parse diverse tree structures into Python for downstream evolutionary analysis.
Yes, this requires Python and the ete3 library installed, as these provide the core environment for integrating NCBITaxa to build and annotate taxonomy topology trees.
Publication-ready visualizations depend on ete3 layout and face configurations, so highly complex phylogenies may require careful customization of tree rendering parameters to achieve optimal output.
tassiovaleAnalyze phylogenetic trees with evolutionary event detection and NCBI taxonomy integration.
OwnLabAIAnalyze phylogenetic trees with Python's ete3 library and NCBITaxa taxonomy annotations.
LogauaEngstromAnalyze and visualize phylogenetic trees with the ETE toolkit.
RamanEbrahimiAnalyze phylogenetic trees and detect evolutionary events using ETE Toolkit.
