Molecular Clock Calculator

The molecular clock hypothesis states that DNA and protein sequences evolve at a rate that is relatively constant over time. This constancy allows genetic divergence to measure the time elapsed since two species shared a common ancestor: T = d / (2 * r), where d is genetic distance and r is the mutation rate. This assumes that neutral mutations accumulate at a steady pace through genetic drift, though mutation rates can vary across different lineages and genomic regions.

Just counting mismatches between two sequences underestimates how much evolution really happened. Over time a single site can mutate more than once, or even flip back to its original base — changes that leave no visible trace. The Jukes-Cantor correction, d = −(3/4)·ln(1 − (4/3)p), converts the observed fraction of differing sites p into the true number of substitutions per site d. At small p the two are nearly equal; they diverge sharply as the sequences grow more different.

Two completely unrelated DNA sequences don't differ at every site — with only four bases (A, T, C, G) they still agree at roughly one site in four by pure chance. So the observed difference p tops out near 0.75, not 1.0. The Jukes-Cantor distance runs to infinity as p approaches 3/4: past this saturation wall, so many multiple hits pile up that the signal is erased, and a single p could correspond to almost any divergence time.