Jukes–Cantor Distance Calculator

Estimate evolutionary divergence between two DNA sequences using the Jukes–Cantor model. Paste aligned sequences or enter counts, choose how to treat gaps and ambiguous bases, and get the corrected distance, mismatch proportion, valid sites, and a 95% confidence interval. Includes FASTA parsing, live validation, and exportable results for transparent, reproducible analysis. Supports case sensitivity checks and nucleotide-only filtering options too.

Use this mode if you already know the mismatch count and n.

Method (JC69)

Observed difference proportion: p = mismatches / n

d = -¾ · ln( 1 - 4p/3 )

Valid for 0 ≤ p < 0.75. If p ≥ 0.75 the correction is undefined (saturation).

FAQs
It is a correction that converts the observed mismatch proportion into an estimate of evolutionary substitutions per site under equal base frequencies and equal mutation rates among nucleotides.
At p ≥ 0.75 the term inside the logarithm becomes non‑positive. This indicates multiple hits saturate the signal and JC69 cannot resolve the true distance.
You can ignore gaps (“-” or “.”), skip ambiguous IUPAC codes like N/R/Y, and optionally restrict comparison to A/C/G/T only to avoid bias from uncertain sites.
The tool compares up to the shorter length and applies your filters. A warning appears if many sites are skipped, suggesting you review alignment quality.
Using the delta method: SE(d) ≈ √(p(1−p)/n) divided by (1−4p/3), then a normal 95% CI is d ± 1.96·SE. Near saturation the SE grows large, reflecting uncertainty.
Yes. U is automatically converted to T so you can paste RNA sequences and evaluate them as DNA for JC69.
Yes. After computing, click “Export CSV” to download a file containing mode, n, mismatches, p, JC69 distance, standard error, and 95% CI.
Results

Enter sequences or counts and press Compute to see results.

Tips
  • For best results, input aligned sequences from a reliable multiple alignment tool.
  • Use the A/C/G/T‑only toggle to avoid counting ambiguous positions.
  • Export CSV to archive your analysis and share it with collaborators.

Important Note: All the Calculators listed in this site are for educational purpose only and we do not guarentee the accuracy of results. Please do consult with other sources as well.