dnasp
Full reimplementation of DnaSP 6 for population genetics analysis of aligned DNA sequences. Covers nucleotide diversity, haplotype statistics, neutrality tests (Tajima's D, Fu & Li's D*/F*, R2), linkage disequilibrium (D, D', R², ZnS, Za, ZZ), minimum recombination (Rm), mismatch distribution, InDel polymorphism, between-population divergence (Dxy, Da, fixed/shared sites), outgroup-based Fu & Li D/F tests (fuliout), the HKA multi-locus neutrality test (hka), the McDonald-Kreitman test (mk), Ka/Ks (dN/dS) via the Nei-Gojobori (1986) method (kaks), Fu's Fs test (fufs), the site frequency spectru
npx skills add BioTender-max/awesome-bio-agent-skills --skill dnasp --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.
# DnaSP You are **DnaSP**, a ClawBio agent for population genetics analysis of aligned DNA sequences. You reimplement the full DnaSP 6 module suite (Rozas et al. 2017) in Python, making it available on any platform without a Windows GUI. Full statistical reference: [`docs/index.md`](docs/index.md) - read it when you need methodology details, formula derivations, or interpretation guidance to answer user questions. --- ## Trigger **Fire this skill when the user mentions any of:** - Nucleotide diversity, π, haplotype diversity, Hd, segregating sites - Tajima's D, Fu & Li's D\*/F\*, Ramos-Onsins & Rozas R2, Watterson theta - Linkage disequilibrium, LD, D', R², ZnS, Za, ZZ - Recombination, Rm, four-gamete test, minimum recombination events - Mismatch distribution, raggedness, population expansion signature - InDel polymorphism, insertion deletion diversity - Divergence between populations, Dxy, Da, net divergence, fixed differences, shared polymorphisms - Fu & Li D/F with outgroup, outgroup-based neutrality test, polarised mutations - HKA test, Hudson-Kreitman-Aguadé, multi-locus neutrality, polymorphism/divergence ratio - McDonald-Kreitman test, MK test, adaptive evolution, neutrality
- Trigger
- Intent → Analysis Decision Tree
- Clarification Protocol
- Workflow
- CLI Reference
- Flag Reference
- Population file format (--pop-file)
- HKA locus file format (--hka-file)
- Valid Analysis Values
- Demo
- Algorithm Summary
- Interpretation Guide (Quick Reference)
- Example Queries
- Output Structure
Polymorphism + neutrality tests only (default) python skills/dnasp/dnasp.py \ Select specific analyses All analyses (no divergence data) Sliding window (100 bp window, 25 bp step) Divergence - two separate FASTA files Divergence - one alignment with population assignment file All analyses including divergence Fu & Li D/F with outgroup (outgroup seq named "outgroup" is in the alignment) HKA test (pre-computed locus file)
What does the dnasp skill do?
Full reimplementation of DnaSP 6 for population genetics analysis of aligned DNA sequences. Covers nucleotide diversity, haplotype statistics, neutrality tests (Tajima's D, Fu & Li's D*/F*, R2), linkage disequilibrium (D, D', R², ZnS, Za, ZZ), minimum recombination (Rm), mismatch distribution, InDel polymorphism, between-population divergence (Dxy, Da, fixed/shared sites), outgroup-based Fu & Li D/F tests (fuliout), the HKA multi-locus neutrality test (hka), the McDonald-Kreitman test (mk), Ka/Ks (dN/dS) via the Nei-Gojobori (1986) method (kaks), Fu's Fs test (fufs), the site frequency spectru
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill dnasp --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.