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alterlab-etetoolkit

85 / 100 · Low risk

Fine to try.

By AlterLab-IEU/AlterLab-Academic-Skills (GitHub) · research · 87 stars · scanned at commit 3ab6d03

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. Part of the AlterLab Academic Skills suite.

Works with any agent that supports SKILL.md skills.

What this skill can do

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'alterlab-etetoolkit' ] || [ -L ~/.agents/skills/'alterlab-etetoolkit' ]; then echo 'A skill folder named alterlab-etetoolkit already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/AlterLab-IEU/AlterLab-Academic-Skills' "$d" && git -C "$d" checkout --quiet '3ab6d034385ec4fedc3f6f4099292d4e91f60300' -- 'skills/bioinformatics/alterlab-etetoolkit' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bioinformatics/alterlab-etetoolkit' ~/.agents/skills/'alterlab-etetoolkit' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'alterlab-etetoolkit' ~/.claude/skills/'alterlab-etetoolkit' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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