package phylogenetics

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Parameters

module A : Alphabet.S
module Align : Alignment with type base := A.t
module E : Site_evolution_model.S with type mat := A.matrix and type vec := A.vector

Signature

val felsenstein_single : ?shift:(float -> float -> A.vector -> A.vector * float) -> E.param -> site:int -> Phylogenetic_tree.t -> Align.t -> float

Single-site. felsenstein without underflow prevention.

val felsenstein_single_shift : ?threshold:float -> E.param -> site:int -> Phylogenetic_tree.t -> Align.t -> float

Single-site felsenstein with underflow prevention (configure threshold through threshold parameter).

val felsenstein_noshift : E.param -> Phylogenetic_tree.t -> Align.t -> float

Multisite felsenstein without underflow prevention.

val felsenstein : E.param -> Phylogenetic_tree.t -> Align.t -> float

Multisite felsenstein with underflow prevention (use this by default).