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bio-comparative-genomics-gene-tree-species-tree-reconciliation

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Check before installing.

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

Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signals…

Works with any agent that supports SKILL.md skills.

What this skill can do

Safer alternatives

Low-risk skills in the same category (other) that look related. Check that one does what you need.

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