/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 two-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 pre-aligned FASTA/NEXUS or a multi-sample VCF (one MSA per CHROM); outputs DnaSP-compatible TSV and a Markdown report. license: MIT metadata: version: "0.5.0" 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: vcf

type: file format:

• vcf

description: >- Multi-sample VCF (--vcf). Converted to one aligned MSA per CHROM (biallelic SNPs only; phased -> haplotype rows). Alternative to --input. Optional --region CHROM, --vcf-merge to pool all CHROMs. required: false

• 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: whitespace-separated, exactly two loci, columns locus n S L_poly D [L_div] [chrom]. 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

• name: genetic_code

type: string description: >- Codon table for mk/kaks/codon: "standard" or "vertebrate-mitochondrial" (TGA=Trp, AGA/AGG=stop, ATA=Met; for COII/cytb/ND-type loci). Default: standard. 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
• two-locus neutrality
• polymorphism divergence ratio
• McDonald-Kreitman test
• MK test
• adaptive evolution test
• alpha McDonald-K