package phylogenetics

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Parameters

module A : Alphabet.S_int

Signature

type t = A.matrix
val make : (A.t -> A.t -> float) -> t
val jc69 : unit -> t
val gtr : equilibrium_frequencies:A.vector -> transition_rates:Linear_algebra.vec -> t
val stationary_distribution : t -> A.vector

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

val 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.

val scale : t -> t

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