Phylogenetic Distance Calculator
Calculate evolutionary distance between DNA sequences using p-distance and Jukes-Cantor correction.
Find sequence similarity, number of substitutions, and expected 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.