Manipulate, annotate, and render phylogenetic trees programmatically with the ETE Toolkit (ete3) — parse and edit Newick/NHX, detect duplication/speciation events, infer orthology and paralogy, query NCBI taxonomy, and export PDF/SVG figures. Use when traversing or reformatting tree files, doing phylogenomic comparative analysis, or producing publication tree graphics in Python.
Install
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-etetoolkitnpx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-etetoolkit -a claude-code -gnpx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-etetoolkit -a codex -ggemini skills install https://github.com/AlterLab-IEU/AlterLab-Academic-Skills.git --path skills/bioinformatics/alterlab-etetoolkitgh skill install AlterLab-IEU/AlterLab-Academic-Skills alterlab-etetoolkitgit clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-Skills /tmp/AlterLab-IEU__AlterLab-Academic-Skills
mkdir -p ~/.claude/skills ~/.agents/skills
cp -R /tmp/AlterLab-IEU__AlterLab-Academic-Skills/skills/bioinformatics/alterlab-etetoolkit ~/.claude/skills/alterlab-etetoolkit # Claude Code
cp -R /tmp/AlterLab-IEU__AlterLab-Academic-Skills/skills/bioinformatics/alterlab-etetoolkit ~/.agents/skills/alterlab-etetoolkit # Codex, Cursor, Gemini CLI, Copilot, OpenCode