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bio-comparative-genomics-genome-distance-and-species-delineation

75 / 100 · Review before installing

Check before installing.

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

Compute genome-to-genome distances (ANI, AAI, dDDH, k-mer Mash) and assign taxonomic classifications using skani (Shaw 2023), FastANI (Jain 2018), pyani / pyANI ANIb / ANIm, OrthoANI (Lee 2016), AAI (amino-acid identity), dDDH via TYGS / GGDC, GTDB-Tk (Chaumeil 2020 standard prokaryote taxonomy), and Mash MinHash (Ondov 2016). Use when delineating prokaryote species (95% ANI threshold; Jain 2018 Nat Commun 9:5114), assigning genomes to GTDB taxonomy with ANI radius, computing genome similarity …

Works with any agent that supports SKILL.md skills.

What this skill can do

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Install

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

if [ -e ~/.agents/skills/'bio-comparative-genomics-genome-distance-and-species-delineation' ] || [ -L ~/.agents/skills/'bio-comparative-genomics-genome-distance-and-species-delineation' ]; then echo 'A skill folder named bio-comparative-genomics-genome-distance-and-species-delineation 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 "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-comparative-genomics-genome-distance-and-species-delineation' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-comparative-genomics-genome-distance-and-species-delineation' ~/.agents/skills/'bio-comparative-genomics-genome-distance-and-species-delineation' && 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-comparative-genomics-genome-distance-and-species-delineation' ~/.claude/skills/'bio-comparative-genomics-genome-distance-and-species-delineation' (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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