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bio-phylo-tree-manipulation

85 / 100 · Low risk

Fine to try.

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

Edit phylogenetic tree structure with Biopython Bio.Phylo, and treat rooting as a separate statistical inference rather than a display choice. Covers why most inference returns an unrooted tree so placing the root creates every ancestor/descendant and basal claim; why a distant or lonely outgroup misroots inside the ingroup via long-branch attraction; the outgroup/midpoint/MAD/MinVar/non-reversible-likelihood rooting tradeoffs; why pruning must suppress degree-2 nodes and sum their branch lengt…

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-manipulation' ] || [ -L ~/.agents/skills/'bio-phylo-tree-manipulation' ]; then echo 'A skill folder named bio-phylo-tree-manipulation 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 "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-phylo-tree-manipulation' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-phylo-tree-manipulation' ~/.agents/skills/'bio-phylo-tree-manipulation' && 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-manipulation' ~/.claude/skills/'bio-phylo-tree-manipulation' (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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