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bio-phylo-tree-io

85 / 100 · Low risk

Fine to try.

By lilinji/GeneTind-Life-Skills (GitHub) · other · 17 stars · scanned at commit 908229c

Read, write, and convert phylogenetic tree files with Biopython Bio.Phylo, and choose an annotation-preserving parser (treeio, DendroPy) when metadata matters. Covers why a tree file is a lossy serialization, why format conversion silently drops BEAST/MrBayes node annotations (posteriors, HPD intervals, rates), the Newick support-vs-label ambiguity that mislabels bootstrap values, and the Nexus TRANSLATE and rooted/unrooted traps. Use when parsing Newick, Nexus, NHX, phyloXML, or NeXML, convert…

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/'bio-phylo-tree-io' ] || [ -L ~/.agents/skills/'bio-phylo-tree-io' ]; then echo 'A skill folder named bio-phylo-tree-io already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/lilinji/GeneTind-Life-Skills' "$d" && git -C "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-phylo-tree-io' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-phylo-tree-io' ~/.agents/skills/'bio-phylo-tree-io' && 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/'bio-phylo-tree-io' ~/.claude/skills/'bio-phylo-tree-io' (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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