Phylogenetic Distance Calculator
Calculate evolutionary distance between DNA sequences using p-distance and Jukes-Cantor correction.
Returns similarity, substitutions, and divergence time.
Evolutionary Distance Evolutionary (phylogenetic) distance measures how diverged two sequences are. The simplest metric is p-distance: p = number of differences / total sites compared. However, p-distance underestimates actual divergence because back-mutations and parallel mutations are invisible.
Jukes-Cantor Correction The Jukes-Cantor (JC69) model corrects p-distance for multiple hits at the same site. d = −(3/4) × ln(1 − 4p/3) Where p = observed proportion of different sites (p-distance). This assumes equal substitution rates among all 4 nucleotides. Derived by Thomas Jukes and Charles Cantor (USA, 1969), the simplest neutral model.
Interpretation d = 0: sequences are identical. d = 0.1: about 10% corrected divergence (moderate similarity). d = 0.2: substantial divergence, sequences still alignable. d > 0.5: highly diverged, long evolution and extensive multiple hits. The JC correction breaks down above p ≈ 0.75 (mathematical limit is 3/4).
Percent Identity vs Distance % identity = (1 − p) × 100 ≥ 97% identity: same species (16S rRNA threshold for bacteria) 90–97%: closely related species < 70%: likely different genera
Molecular Clock If the substitution rate is known, divergence time can be estimated. Time in years = d / (2 × substitution rate per site per year). Divide by 1,000,000 for Mya. The factor of 2 is there because both lineages have been changing since they split, so the distance you measure accumulated along two branches, not one.
Getting the units right is where most people trip. The rate you enter is per site per year, and real rates are tiny. Mammalian mitochondrial DNA is usually quoted as about 2% divergence per million years, and that works out to 1e-8 per site per year, not 0.02. Enter 0.02 and the calculator will faithfully tell you two lineages split about a year ago.
| Marker | Rough rate per site per year |
|---|---|
| Mitochondrial DNA, mammals (cytochrome b) | 1e-8 |
| Nuclear genes, mammals (average) | 1e-9 to 2e-9 |
| 16S rRNA, bacteria | 1e-10 to 5e-10 |
| ITS, fungi and plants | 1e-9 to 1e-8 |
Rates vary widely by gene and by organism, so treat those as starting points rather than constants. If your marker is not in the table, look up a published rate for that gene in that group before trusting any date the calculator gives you.
How we build and check this calculator
This calculator runs entirely in your browser, so the numbers you enter stay on your device. The math behind it is written by hand and tested against worked examples and standard references before the page goes live.
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