The Cavender-Farris-Neyman (CFN) Model is a Markov model of base substitution. It also known as the binary Jukes-Cantor model. 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.

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