package phylogenetics

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package phylogenetics
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Library
Module
Module type
Parameter
Class
Class type
include sig ... end
val make : (Nucleotide.t -> Nucleotide.t -> float) -> t
val jc69 : unit -> t

Jukes and Cantor 1969

val gtr : equilibrium_frequencies:Nucleotide.vector -> transition_rates:Linear_algebra.vec -> t

Generalised Time-Reversible model

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 : equilibrium_frequencies:Nucleotide.vector -> transition_rate:float -> transversion_rate:float -> t