protein-phylogeny
Protein (gene) phylogeny inference pipeline: generates a .qmd analysis script that performs alignment, optional trimming, and tree building. Use when building phylogenetic trees from protein sequences, aligning protein families, running IQ-TREE or MAFFT for phylogenetics, or when the user says "gene tree" or "protein tree." Covers single domains, whole proteins, and multi-domain proteins across deep evolutionary distances (sponges, animals, eukaryotes). Do NOT load for nucleotide-only phylogenies, species trees from concatenated matrices, or tree visualization (use tree-formatting skill for th
npx skills add majiayu000/claude-skill-registry --skill protein-phylogeny --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Protein Phylogeny Inference Pipeline for building protein phylogenies across deep evolutionary distances. Designed for single domains, whole single-domain proteins, and multi-domain proteins, from ~10 to several thousand sequences, spanning sponges to all eukaryotes. **If the user says "gene tree" they may mean protein sequences.** Confirm if ambiguous, or inspect the input sequences (amino acid alphabet vs nucleotide). --- ## Overview: Two-Phase Workflow This skill generates a **reproducible .qmd analysis script** (Python) rather than running commands directly. The workflow is: 1. **Discuss** — Resolve all pipeline decisions with the user (input sequences, algorithm, model tier, trimming, etc.) 2. **Generate** — Write a complete `.qmd` script encoding all decisions as configuration variables, following quarto-docs and script-organization skill conventions 3. **Render** — User renders with `quarto render` (or Claude renders it), producing all outputs in `outs/<subdirectory>/XX_script_name/` One script per major deliverable (one protein family or domain tree). All pipeline steps go in one `.qmd` unless there is a strong reason to split. --- ## Phase 1: Discussion Resolve these que
- Overview: Two-Phase Workflow
- Phase 1: Discussion
- 1. Input validation
- 2. Minimum length cutoff
- 3. CD-HIT redundancy reduction (optional, off by default)
- 4. MAFFT algorithm selection
- 5. Trimming (optional, off by default)
- 6. IQ-TREE tier selection
- 7. Branch support
- 8. No automated outlier removal
- Phase 2: Script Generation
- Naming and placement
- .qmd structure
- Key patterns
source ~/miniconda3/etc/profile.d/conda.sh && conda activate <env> quarto render scripts/<subdirectory>/XX_name.qmd --output-dir outs/<subdirectory>/XX_name/
What does the protein-phylogeny skill do?
Protein (gene) phylogeny inference pipeline: generates a .qmd analysis script that performs alignment, optional trimming, and tree building. Use when building phylogenetic trees from protein sequences, aligning protein families, running IQ-TREE or MAFFT for phylogenetics, or when the user says "gene tree" or "protein tree." Covers single domains, whole proteins, and multi-domain proteins across deep evolutionary distances (sponges, animals, eukaryotes). Do NOT load for nucleotide-only phylogenies, species trees from concatenated matrices, or tree visualization (use tree-formatting skill for th
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill protein-phylogeny --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.