package phylogenetics

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Module Rate_matrix.MakeSource

Parameters

module A : Alphabet.S_int

Signature

Sourceval make : (A.t -> A.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.

Sourceval make_symetric : (A.t -> A.t -> float) -> t
Sourceval jc69 : unit -> t

Jukes and Cantor 1969

Sourceval gtr : stationary_distribution:A.vector -> exchangeabilities:A.matrix -> t

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

Sourceval stationary_distribution : t -> A.vector

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

Sourceval scaled_rate_matrix : A.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.

Sourceval scale : t -> t

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