package phylogenetics

  1. Overview
  2. Docs
package phylogenetics
Legend:
Library
Module
Module type
Parameter
Class
Class type

Parameters

module A : Alphabet.S_int
module BI : Branch_info

Signature

val transition_matrix : (BI.t -> A.matrix) -> BI.t -> A.matrix
val site_exponential_method : Gsl.Rng.t -> ('n, 'l, BI.t) Tree.t -> root:A.t -> transition_matrix:(BI.t -> A.matrix) -> ('n * A.t, 'l * A.t, BI.t) Tree.t
val branch_gillespie_direct : Gsl.Rng.t -> start_state:A.t -> rate_matrix:A.matrix -> branch_length:float -> init:'a -> f:('a -> A.t -> float -> 'a) -> 'a
val site_gillespie_direct : Gsl.Rng.t -> ('n, 'l, BI.t) Tree.t -> root:A.t -> rate_matrix:(BI.t -> A.matrix) -> ('n * A.t, 'l * A.t, BI.t) Tree.t
val site_gillespie_first_reaction : Gsl.Rng.t -> ('n, 'l, BI.t) Tree.t -> root:A.t -> rate_matrix:(BI.t -> A.matrix) -> ('n * A.t, 'l * A.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:A.t array -> rate_vector:(BI.t -> A.t array -> int -> float A.table) -> ('n * A.t array, 'l * A.t array, BI.t) Tree.t
val hmm0 : Gsl.Rng.t -> len:int -> dist:(int -> float A.table) -> A.t array