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, 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 (Mya) = d / (2 × substitution rate per site per year) Mitochondrial DNA: ~2% divergence per million years (cytochrome b, mammals). 16S rRNA evolves much slower; ITS (fungi/plants) faster. Substitution rates vary widely by gene and organism.
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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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