bio-phylogenomics
Build marker gene alignments and phylogenetic trees.
npx skills add BioTender-max/awesome-bio-agent-skills --skill bio-phylogenomics --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.
# Bio Phylogenomics Build marker gene alignments and phylogenetic trees. ## Instructions 1. Extract marker genes or SSU rRNA sequences. 2. Align with MAFFT v7.5+ and trim with trimAl v1.4 (or ClipKIT when phylogenetically-informed trimming is preferred). 3. Build ML trees with support values. Choose by objective first, then leaf count: - Exploratory placement, benchmark iterations, reference-set screening, or any time-bounded analysis: use VeryFastTree v4.0 first, even below ~2,000 taxa. Prefer `VeryFastTree -boot 1000 -threads <n> < alignment.faa > tree.nw` for proteins and add `-nt` for nucleotide alignments. - Final or publication-quality trees up to ~2,000 taxa: IQ-TREE v3 (v3.1.2+) for comprehensive model selection, MAST/GTRpmix, UFBoot/SH-aLRT, and defensible final inference. - Above ~2,000 taxa, or when memory/runtime is uncertain: VeryFastTree v4.0 (multi-threaded, SIMD, `-disk-computing` for very large trees). - Use `iqtree3 -fast` only when VeryFastTree is unavailable or a project explicitly requires IQ-TREE-compatible exploratory output; record that fallback in the report. 4. Post-process trees with ETE v4 (`ete4`): - Compute tree statistics (branch lengths, distances, t
- Instructions
- Quick Reference
- Input Requirements
- Output
- Quality Gates
- Examples
- Example 1: Expected input layout
- Troubleshooting
What does the bio-phylogenomics skill do?
Build marker gene alignments and phylogenetic trees.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill bio-phylogenomics --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 BioTender-max/awesome-bio-agent-skills, a repository with 135 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.