/dnasp

--- name: dnasp description: Population genetics of pre-aligned DNA sequences or multi-sample VCFs using selected DnaSP 6 methods. Use for diversity, neutrality statistics, linkage disequilibrium, InDel polymorphism, divergence, MK, Ka/Ks and codon usage; not alignment, phasing or clinical interpretation. license: MIT metadata: version: 0.6.1 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: false cli_flag: --input

• 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 cli_flag: --vcf

• 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 cli_flag: --input2

• name: pop_file

type: file format:

• tsv
• txt

description: 'Population assignment file: one row per sequence, tab-separated (sequence_name<TAB>population_name). Required for Fst; alternative to --input2 for divergence.' required: false cli_flag: --pop-file

• name: outgroup

type: string description: Unique sequence identifier removed from the ingroup. Required for fuliout, mk and faywu; also polarises SFS/TsTv and selects ingroup-versus-outgroup Ka/Ks. required: false cli_flag: --outgroup

• 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 cli_flag: --hka-file

• name: analyses

type: string description: Comma-separated polymorphism, ld, recombination, popsize, indel, divergence, fuliout, hka, mk, kaks, fufs, sfs, tstv, codon, faywu, fst; or all. Polymorphism runs with alignment input. required: false cli_flag: --analysis

• name: window_size

type: integer description: Sliding window size in bp (0 = whole alignment only, default 0) required: false cli_flag: --window

• name: step_size

type: integer description: Sliding window step in bp (default = window_size) required: false cli_flag: --step

• 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 cli_flag: --genetic-code

• name: n_sim

type: integer description: Coalescent replicates for whole-region P-values of Tajima's D, R2 and Fu's Fs (0 = no simulation, default). 10000 is typical. required: false cli_flag: --n-sim

• name: sim_given

type: string description: 'Simulation conditioned on the observed segregating sites ("S", default) or on Watterson''s theta ("theta").' required: false cli_flag: --sim-given

• name: sim_seed

type: integer description: Seed for --n-sim; generated and recorded when omitted. required: false cli_flag: --sim-seed outputs:

• name: report

type: file format:

• md

description: Markdown analysis report with statistics and interpretation

• name: results_table

type: file format:

• tsv

description: Polymorphism and sliding-window TSV only; other modules appear in report.md.

• name: result

type: file format:

• json

description: ClawBio result.json envelope (skill, version, input checksum, headline summary, the summary.json payload plus artifact list, chat_summary_lines and preferred_artifacts for the runner). A multi-CHROM VCF run writes one envelope per CHROM directory and a root envelope that summarises them with relative paths.

• name: summary

type: file format:

• json

description: Module summaries (global and per-window statistics with DnaSP midpoints, LD/recombination/mismatch/InDel/divergence/MK/Ka-Ks/codon results including named per-sequence ENC); LD pair grids are in ld_pairs, not here.

• 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: Archived inputs, commands.sh, environment.yml, manifest.json and output-relative checksums.sha256. dependencies: python: '>=3.10' packages:

• matplotlib>=3.7
• numpy>=1.24
• pandas>=2.0
• opentelemetry-sdk>=1.20

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
• win32

install:

• kind: pip

package: matplotlib>=3.7

• kind: pip

package: numpy>=1.24

• kind: pip