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PhylogeneticTrees :: CFNmodel

CFNmodel -- the model corresponding to the Cavender-Farris-Neyman model or binary Jukes Cantor


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 $$\begin{pmatrix} \alpha&\beta\\ \beta&\alpha \end{pmatrix}$$

See also

For the programmer

The object CFNmodel is an instance of the type Model.