package phylogenetics

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Module
Module type
Parameter
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Class type

Parameters

module BI : Branch_info

Signature

include sig ... end
val site_exponential_method : Gsl.Rng.t -> ('n, 'l, BI.t) Tree.t -> root:Phylogenetics.Mutsel.NSCodon.t -> transition_matrix:(BI.t -> Phylogenetics.Mutsel.NSCodon.matrix) -> ('n * Phylogenetics.Mutsel.NSCodon.t, 'l * Phylogenetics.Mutsel.NSCodon.t, BI.t) Tree.t
val branch_gillespie_direct : Gsl.Rng.t -> start_state:Phylogenetics.Mutsel.NSCodon.t -> rate_matrix:Phylogenetics.Mutsel.NSCodon.matrix -> branch_length:float -> init:'a -> f:('a -> Phylogenetics.Mutsel.NSCodon.t -> float -> 'a) -> 'a
val site_gillespie_direct : Gsl.Rng.t -> ('n, 'l, BI.t) Tree.t -> root:Phylogenetics.Mutsel.NSCodon.t -> rate_matrix:(BI.t -> Phylogenetics.Mutsel.NSCodon.matrix) -> ('n * Phylogenetics.Mutsel.NSCodon.t, 'l * Phylogenetics.Mutsel.NSCodon.t, BI.t) Tree.t
val site_gillespie_first_reaction : Gsl.Rng.t -> ('n, 'l, BI.t) Tree.t -> root:Phylogenetics.Mutsel.NSCodon.t -> rate_matrix:(BI.t -> Phylogenetics.Mutsel.NSCodon.matrix) -> ('n * Phylogenetics.Mutsel.NSCodon.t, 'l * Phylogenetics.Mutsel.NSCodon.t, BI.t) Tree.t
val sequence_gillespie_direct : Gsl.Rng.t -> ('n, 'l, BI.t) Tree.t -> update_iterator:(n:int -> pos:int -> (int -> unit) -> unit) -> root:Phylogenetics.Mutsel.NSCodon.t array -> rate_vector: (BI.t -> Phylogenetics.Mutsel.NSCodon.t array -> int -> float Phylogenetics.Mutsel.NSCodon.table) -> ('n * Phylogenetics.Mutsel.NSCodon.t array, 'l * Phylogenetics.Mutsel.NSCodon.t array, BI.t) Tree.t
val hmm0 : Gsl.Rng.t -> len:int -> dist:(int -> float Phylogenetics.Mutsel.NSCodon.table) -> Phylogenetics.Mutsel.NSCodon.t array
val alignment : Gsl.Rng.t -> (_, _, BI.t) Tree.t -> root:Phylogenetics.Mutsel.NSCodon.t array -> rate_matrix:(int -> BI.t -> Mutsel.NSCodon_rate_matrix.t) -> Dna.t list
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