The Jukes-Cantor (JK) Model is a Markov model of base substitution. It assumes the root distribution vectors describe all bases occurring uniformly in the ancestral sequence. It also assumes that the rate of all specific base changes is the same. Thus the rates of bases changes A-G, A-T and A-C are the same.

The transition matrix has the form $$\begin{pmatrix} \alpha&\beta&\beta&\beta\\ \beta&\alpha&\beta&\beta\\ \beta&\beta&\alpha&\beta\\ \beta&\beta&\beta&\alpha \end{pmatrix}$$