The Jukes–Cantor model is a common model of DNA sequence evolution. It is often also called the JC69 model after an article published by the two authors in 1969. The model characterises the probability that a single nucleotide (A, T, G, or C) in an ancestral sequence evolves into a given nucleotide in a descendant sequence given a single parameter, 𝝂, which is related to both the time passed between the two states of the sequence as well as the mutation rate. The probability that any of the nucleotides, say A, evolves into a specific different nucleotide, say T, is given by ¼ – ¼ exp(–4𝝂 / 3). The probability that the same nucleotide is observed in the descendant taxon is given by ¼ + ¾ exp(–4𝝂 / 3).

The base frequencies, i.e., the probabilities of observing any given nucleotide in the ancestral sequence, are assumed to be uniform: (¼, ¼, ¼, ¼).

Alternative sequence evolution models include, for example, the K80 and F81 models, see Lemey 2009.


– Jukes, Thomas H., and Charles R. Cantor. 1969. “Evolution of Protein Molecules.” In Mammalian Protein Metabolism, edited by Hamish N. Munro, 21–132. New York: Academic Press.
– Lemey, Philippe, Marco Salemi, and Anne-Mieke Vandamme, eds. 2009. The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing. 2nd ed. Cambridge: Cambridge University Press

In other languages

DE: Jukes-Cantor-Modell
FR: modèle de Jukes-Cantor
IT: modello di Jukes-Cantor


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