package phylogenetics

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package phylogenetics
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Module Phylogenetics.Rate_matrixSource

Continuous Time Markov Chain rate matrix

A rate matrix is the infinitesimal generator for a discrete-space continuous time markov process. It is basically a matrix such that all off-diagonal elements are positive and each diagonal element is minus the sum of all other elements in the row.

Sourcemodule type S = sig ... end
Sourcemodule Make (A : Alphabet.S_int) : S with type symbol := A.t and type vector := A.vector and type matrix := A.matrix
Sourcemodule Nucleotide : sig ... end
Sourcemodule Amino_acid : sig ... end
Sourceval make : int -> f:(int -> int -> float) -> Linear_algebra.mat
Sourceval transition_probability_matrix : tau:float -> rates:float array array -> float array array
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