Updated 2mo ago
by Hongda-Zhao
bio-gene-to-reference-tree
Auditable agent skill for resolving protein queries, selecting references, and planning reproducible phylogenetic trees.
20 GitHub stars (20)
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- 6 skills (6 skills found in its SKILL.md files)
- 0 forks (0 forks)
- 2mo ago last update (Last updated 2mo ago)
Install
Skills CLI
npx skills add Hongda-Zhao/bio-gene-to-reference-tree
Asks which skills and agents to install. Just one: npx skills add Hongda-Zhao/bio-gene-to-reference-tree --skill bio-gene-to-reference-tree — add -g for every project.
Claude Code
git clone https://github.com/Hongda-Zhao/bio-gene-to-reference-treecp -r "bio-gene-to-reference-tree/skills/bio-gene-to-reference-tree" ~/.claude/skills/
Copies the bio-gene-to-reference-tree skill into ~/.claude/skills/ for every project (use .claude/skills/ for one project). Repeat for the other skills listed below.
Plugin
/plugin marketplace add Hongda-Zhao/bio-gene-to-reference-tree
Run inside Claude Code if the repository ships a plugin marketplace, then pick plugins from /plugin.
Skills can run code on your machine — read the SKILL.md first.
What it does
In the author's own words, from each skill's SKILL.md.
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bio-gene-to-reference-tree
Build an auditable protein or nucleotide gene tree from an accession, explicitly declared local sequence, or gene, protein, or feature name plus source organism. Use when an agent must choose an environment-appropriate route; resolve metadata and exact NCBI TaxIDs; classify gene-family conservation at an explicit taxonomic scope; curate references and outgroups; align proteins, noncoding DNA or R…
skills/bio-gene-to-reference-tree/ on GitHub (opens in a new tab)SKILL.md -
gene-tree-alignment-and-inference
Plan or review molecule-aware MSA, trimming sensitivity, and FastTree or IQ-TREE2 inference for an approved gene-tree reference set. Use for workflow Steps 6–8 while preserving separate alignment and inference approvals.
.github/skills/ on GitHub (opens in a new tab)gene-tree-alignment-and-inference/ SKILL.md -
gene-tree-environment-routing
Match a gene-tree task to available software and local, browser, SSH, or HPC environments without changing scientific decisions. Use for capability discovery, software alternatives, environment snapshots, route selection, or execution handoff planning.
.github/skills/ on GitHub (opens in a new tab)gene-tree-environment-routing/ SKILL.md -
gene-tree-query-and-scope
Resolve a protein, nucleotide, or CDS accession, local sequence, or name-plus-organism query and define its gene-tree objective. Use for molecule identity, provenance, exact taxonomy, analysis space, ingroup, or deliverable decisions before homolog discovery.
.github/skills/ on GitHub (opens in a new tab)gene-tree-query-and-scope/ SKILL.md -
gene-tree-reference-curation
Discover and review homolog or ortholog candidates, references, clustering, and outgroups for a protein or nucleotide gene tree. Use after query identity and scope are fixed and before sequence alignment begins.
.github/skills/ on GitHub (opens in a new tab)gene-tree-reference-curation/ SKILL.md -
gene-tree-visualization-reporting
Create or review iTOL, ggtree or ggplot2, metadata, literature comparison, and final reporting for an approved gene tree. Use for workflow Steps 9–10 after inference artifacts exist.
.github/skills/ on GitHub (opens in a new tab)gene-tree-visualization-reporting/ SKILL.md
No skill matches that filter.
Review before you install
A skill is a set of instructions and scripts your agent will follow, and it can run code on your machine. Read the SKILL.md and any scripts first — this listing is not a security review.
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