Dn Ds Tools

Configuration File: dn_ds_tools.json Tool Type: Local Tools Count: 1

This page contains all tools defined in the dn_ds_tools.json configuration file.

Available Tools

Sequence_dn_ds (Type: DnDsTool)

Compute dN/dS (Ka/Ks) between two coding sequences via the Nei-Gojobori (1986) estimator with Juk…

Sequence_dn_ds tool specification

Tool Information:

  • Name: Sequence_dn_ds

  • Type: DnDsTool

  • Description: Compute dN/dS (Ka/Ks) between two coding sequences via the Nei-Gojobori (1986) estimator with Jukes-Cantor correction — the standard test for selection: dN/dS > 1 = positive/diversifying, << 1 = purifying, ~ 1 = near-neutral. Give two in-frame, codon-aligned coding sequences inline (‘seq1’/’seq2’) or as single-record FASTA files. Returns dN, dS, the ratio, per-site counts, and an interpretation. Pure Python, no API key. Works for any organisms/genes.

Parameters:

  • seq1 ([‘string’, ‘null’]) (optional) First coding sequence (in-frame, codon-aligned to seq2). DNA/RNA letters.

  • seq2 ([‘string’, ‘null’]) (optional) Second coding sequence (same length/frame as seq1).

  • fasta1_path ([‘string’, ‘null’]) (optional) Alternative to seq1: path to a single-record FASTA

  • fasta2_path ([‘string’, ‘null’]) (optional) Alternative to seq2: path to a single-record FASTA

Example Usage:

query = {
    "name": "Sequence_dn_ds",
    "arguments": {
    }
}
result = tu.run(query)