skills.rest
MubasherMohammed
MubasherMohammedCOMMUNITY
Explore all skills by this author →
WebsiteGitHub

dnasp

Analyze DNA sequences with DnaSP 6 population genetics algorithms.

Updated May 10, 2026
Search Tags:#recombination#divergence#population genetics#DnaSP#DNA sequence analysis#population diversity#neutrality tests#linkage disequilibrium#InDel polymorphism#Fu & Li D/F#HKA test#McDonald-Kreitman test#Ka/Ks#Fu's Fs test#site frequency spectrum#transition/transversion ratio#codon usage bias
One-click install
npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill dnasp
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: dnasp
Source: https://github.com/MubasherMohammed/opencode-BioInfo/tree/main/python/skills/dnasp
Command: npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill dnasp

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires matplotlib, numpy, pandas, scipy, and includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve?

This Skill provides a comprehensive suite of population genetics analysis tools, reimplementing the DnaSP 6 algorithms for analyzing DNA sequences.

Core Features & Use Cases

  • Diversity and Neutrality: Calculate nucleotide diversity, haplotype diversity, and neutrality tests (Tajima's D, Fu & Li's D/F, R2).
  • Linkage Disequilibrium: Analyze D, D', R², ZnS, Za, ZZ, and LD decay.
  • Recombination: Estimate minimum recombination events and detect four-gamete test events.
  • Mismatch Distribution: Study mismatch distribution for population size history.
  • InDel Polymorphism: Analyze insertion/deletion polymorphism events.
  • Divergence: Measure between-population divergence (Dxy, Da, fixed/shared sites).
  • Other Features: Fu & Li D/F with outgroup, HKA multi-locus neutrality test, McDonald-Kreitman test, Ka/Ks (dN/dS), Fu's Fs test, site frequency spectrum (SFS), transition/transversion ratio (tstv), codon usage bias (RSCU, ENC), Fay & Wu's H and Zeng's E, Fst, etc.
  • Use Case: Suppose you have a set of DNA sequences from two different populations and want to compare their genetic diversity and divergence. This Skill can help you compute various statistics to answer these questions.

Quick Start

To perform a basic polymorphism analysis, use the following command:

python skills/dnasp/dnasp.py --input alignment.fas --output results/

Frequently Asked Questions about dnasp

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I calculate nucleotide diversity and run neutrality tests like Tajima's D for DNA sequences?▼

To calculate nucleotide diversity and run neutrality tests like Tajima's D, you can use this Skill which reimplements DnaSP 6 algorithms. It processes DNA sequence alignments to compute diversity metrics and perform statistical tests directly via Python.

Can I analyze linkage disequilibrium and estimate recombination events from a sequence alignment in Python?▼

Yes, you can analyze linkage disequilibrium and estimate recombination events in Python. This Skill calculates LD metrics like D' and R², detects four-gamete test events, and estimates minimum recombination events from DNA sequence alignments.

What is the best way to measure between-population divergence and perform McDonald-Kreitman tests?▼

The best way to measure between-population divergence and perform McDonald-Kreitman tests is using this DnaSP 6 reimplementation. It calculates Dxy, Da, fixed and shared sites, and executes the McDonald-Kreitman test to detect selection from DNA sequence data.

Does this population genetics analysis skill require specific Python dependencies?▼

Yes, this population genetics analysis requires Python 3.10 and specific dependencies. You must have matplotlib, numpy, pandas, and scipy installed to execute the DnaSP 6 algorithms for visualization and statistical analysis of DNA sequences.

How do I compute Ka/Ks ratios and codon usage bias for my DNA sequences?▼

You can compute Ka/Ks ratios and codon usage bias by running this Skill on your DNA sequence alignment. It calculates dN/dS values and codon usage metrics like RSCU and ENC to evaluate selection pressures and codon preferences.

Related Skills

Explore More Data & Analytics Skills→
AradotsoAradotso
5

car-sales-data-engineering-analytics

Process car sales datasets with ETL pipelines and Streamlit dashboards.

Official
Advanced
jackspacejackspace
16

scikit-bio

Analyze biological sequences for microbiome and ecological data interpretation.

Community
Advanced
swaruplabswaruplab
94

gnomad-database

Query gnomAD population allele frequencies and constraint scores via GraphQL.

Community
Intermediate
inflexa-aiinflexa-ai
29

genomic-variants

Execute germline and somatic variant calling with GATK, PLINK2, and VEP.

Official
Advanced