package phylogenetics

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include sig ... end
val make : (Nucleotide.t -> Nucleotide.t -> float) -> t

make f is a matrix such that f i j is the rate of transition from state i to state j. f is called only for i <> j.

val make_symetric : (Nucleotide.t -> Nucleotide.t -> float) -> t
val jc69 : unit -> t
val gtr : stationary_distribution:Nucleotide.vector -> exchangeabilities:Nucleotide.matrix -> t

Generalised Time-Reversible model. exchangeabilities should be a symetric matrix with arbitrary diagonal

val stationary_distribution : t -> Nucleotide.vector

stationary_distribution r numerically computes the asymptotic probability distribution pi of the CTMC defined by r.

val scaled_rate_matrix : Nucleotide.vector -> t -> t

scaled_rate_matrix pi r is a new matrix rate such that the corresponding CTMC has one expected transition per unit of time. In addition, if r is symetrical, the result has pi as stationary distribution.

val scale : t -> t

rescale matrix such that the sum of off-diagonal elements is 1.

val k80 : float -> t
val hky85 : stationary_distribution:Nucleotide.vector -> transition_rate:float -> transversion_rate:float -> t
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