Manipulate phylogenetic trees and detect duplication and speciation events.
npx skills add https://github.com/Hung-3008/agusta --skill etetoolkit-hung-3008
Please help me install this Agent Skill. Skill: etetoolkit Source: https://github.com/Hung-3008/agusta/tree/main/.agents/skills/etetoolkit Command: npx skills add https://github.com/Hung-3008/agusta --skill etetoolkit-hung-3008
Phylogenetic analysis often requires manual scripting to manipulate trees, detect evolutionary events, and integrate taxonomy. This Skill provides a comprehensive toolkit for tree operations, event detection, and visualization to streamline phylogenomic workflows.
Load a gene tree with an alignment, run event detection, and export ortholog groups.
High-intent search queries and answers about installing and using this skill.
Detect duplication and speciation events in a phylogenetic tree by loading a gene tree with an alignment into this toolkit, which automates event detection and derives ortholog groups for downstream studies.
Yes, you can visualize phylogenetic trees with NCBI taxonomy annotations by using NCBITaxa to build taxonomy-informed trees, annotate leaves, and generate publication-ready figures with configurable layouts and styles.
Supported tree formats for phylogenetic analysis and manipulation include Newick, NHX, PhyloXML, and NeXML, allowing you to load, prune, reroot, traverse, and compare trees across diverse datasets.
Yes, you need the ete3 toolkit installed to run phylogenomic workflows and orthology inference, as this Skill relies on ete3 and its optional NCBITaxa, PhyloTree, and Tree APIs for tree operations.
Export ortholog groups from a gene tree analysis by loading the tree with an alignment, running event detection to cluster by speciation, and extracting the derived ortholog groups for downstream studies.
The best way to reroot and prune phylogenetic trees for publication workflows is using this toolkit's tree manipulation functions, which support common formats and prepare topology with taxonomy annotations for figures.
tassiovaleAnalyze phylogenetic trees with evolutionary event detection and NCBI taxonomy integration.
jimmc414Manipulate, analyze, and visualize phylogenetic trees using the ETE3 library.
shushuznParse, transform, and analyze phylogenetic trees with ETE Toolkit.
galeepAnalyze and visualize phylogenetic trees using the ete3 library.
