/dnasp

name: dnasp
description: >-
  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
  spectrum (sfs, folded and outgroup-unfolded), transition/transversion ratio
  (tstv), and codon usage bias  -  RSCU (Sharp & Li 1987) and ENC (Wright 1990)
  (codon). Accepts FASTA or NEXUS input; outputs DnaSP-compatible TSV and a
  Markdown report.
license: MIT
metadata:
  version: "0.4.0"
  author: David De Lorenzo
  domain: molecular-evolution
  tags:
    - population-genetics
    - molecular-evolution
    - DNA-polymorphism
    - neutrality-tests
    - linkage-disequilibrium
    - recombination
    - divergence
    - sequence-analysis
  inputs:
    - name: alignment
      type: file
      format:
        - fasta
        - fas
        - nexus
        - nex
      description: >-
        Aligned DNA sequences (pre-aligned, equal-length). FASTA (including
        DnaSP-style >'name' [comment] headers) or NEXUS (MATCHCHAR, INTERLEAVE).
      required: true
    - name: alignment2
      type: file
      format:
        - fasta
        - fas
        - nexus
        - nex
      description: >-
        Second-population alignment for divergence analysis (--input2).
        Alternative to --pop-file. Sequences must have same length as --input.
      required: false
    - name: pop_file
      type: file
      format:
        - tsv
        - txt
      description: >-
        Population assignment file: one row per sequence, tab-separated
        (sequence_name<TAB>population_name). Alternative to --input2.
      required: false
    - name: outgroup
      type: string
      description: >-
        Sequence name in the alignment to use as outgroup for the fuliout analysis.
        The named sequence is removed from the ingroup and used to polarise mutations.
      required: false
    - name: hka_file
      type: file
      format:
        - tsv
        - txt
      description: >-
        HKA locus file: tab-separated (locus<TAB>S<TAB>D<TAB>n) where S = segregating
        sites in ingroup, D = fixed differences to outgroup, n = ingroup sample size.
        Required for --analysis hka.
      required: false
    - name: analyses
      type: string
      description: >-
        Comma-separated list of analyses to run, or "all". Options:
        polymorphism, ld, recombination, popsize, indel, divergence, fuliout, hka, mk, kaks, fufs, sfs, tstv, codon.
        Default: polymorphism.
      required: false
    - name: window_size
      type: integer
      description: Sliding window size in bp (0 = whole alignment only, default 0)
      required: false
    - name: step_size
      type: integer
      description: Sliding window step in bp (default = window_size)
      required: false
  outputs:
    - name: report
      type: file
      format:
        - md
      description: Markdown analysis report with statistics and interpretation
    - name: results_table
      type: file
      format:
        - tsv
      description: DnaSP-compatible tab-delimited results
    - name: ld_pairs
      type: file
      format:
        - tsv
      description: Pairwise LD table (only when --analysis ld is active)
    - name: figures
      type: directory
      description: Sliding-window plots, LD decay scatter, mismatch histogram (PNG)
    - name: reproducibility
      type: directory
      description: commands.sh, environment.yml, SHA-256 checksums
  dependencies:
    python: ">=3.10"
    packages:
      - matplotlib>=3.7
  demo_data:
    - path: examples/demo_simple.fas
      description: Synthetic 6-sequence × 10-bp alignment with known statistics
    - path: examples/demo_rp49.fas
      description: rp49 region, 17 Drosophila sequences, 300 bp
  endpoints:
    cli: >-
      python skills/dnasp/dnasp.py --input {alignment} --analysis {analyses} --output {output_dir}
  openclaw:
    requires:
      bins:
        - python3
    always: false
    emoji: ""
    homepage: https://github.com/ClawBio/ClawBio
    os:
      - darwin
      - linux
    install:
      - kind: pip
        package: matplotlib
    trigger_keywords:
      - nucleotide diversity
      - Tajima's D
      - DNA polymorphism
      - population genetics sequences
      - haplotype diversity
      - DnaSP
      - segregating sites
      - Fu and Li test
      - neutrality test alignment
      - Watterson theta
      - linkage disequilibrium
      - recombination events
      - mismatch distribution
      - population expansion
      - InDel polymorphism
      - divergence between populations
      - Dxy Da net divergence
      - fixed differences populations
      - Ramos-Onsins Rozas R2
      - Fu Li D F outgroup
      - outgroup polarised mutations
      - HKA test neutrality
      - Hudson Kreitman Aguade
      - multi-locus neutrality
      - polymorphism divergence ratio
      - McDonald-Kreitman test
      - MK test
      - adaptive evolution test
      - alpha McDonald-Kreitman
      - neutrality index NI
      - direction of selection DoS
      - Ka/Ks
      - dN/dS
      - omega synonymous nonsynonymous
      - synonymous substitution rate
      - nonsynonymous substitution rate
      - coding sequence neutrality
      - Nei-Gojobori method
      - Fu's Fs test
      - Fu 1997 Fs
      - site frequency spectrum
      - SFS folded unfolded
      - allele frequency spectrum
      - singleton excess
      - minor allele frequency distribution

DnaSP

You are **DnaSP**, a ClawBio agent for population genetics ana