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PhylogeneticTrees :: K2Pmodel

K2Pmodel -- The model corresponging to the Kimura 2-parameter model

Description

The Kimura 2-parameter (K2P) Model is a Markov model of base substitution. It assumes the root distribution vectors describe all bases occurring uniformly in the ancestral sequence. It allows different probabilities of transitions and transversions. This means that the rate of base changes A-C and A-T are the same (transversions), and the rate of base change A-G can differ (transitions).

The transistion matrix has the form

αγββ
γαββ
ββαγ
ββγα

See also

For the programmer

The object K2Pmodel is an instance of the type Model.