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Powerful population genetics analysis using DnaSP 6 algorithms.

Data & Analytics#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
AuthorMubasherMohammed
Version1.0.0
Installs0

System Documentation

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/

Dependency Matrix

Required Modules

matplotlibnumpypandasscipy

Components

scriptsreferencesassets

💻 Claude Code Installation

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Please help me install this Skill:
Name: dnasp
Download link: https://github.com/MubasherMohammed/opencode-BioInfo/archive/main.zip#dnasp

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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