package phylogenetics

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phylogenetics
- Phylogenetics
  - Alignment
    
    Fasta
    
    Make
    
    S
    
    Phylip
  - Alphabet
    
    Make
    
    Matrix
    
    Table
    
    Vector
    
    X
    
    S
    
    Matrix
    
    Table
    
    Vector
    
    S_int
    
    Matrix
    
    Table
    
    Vector
  - Amino_acid
    
    Matrix
    
    Table
    
    Vector
  - Birth_death
  - Bppsuite
    
    Cmd
  - Codon
    
    Genetic_code
    
    NS
    
    Matrix
    
    Table
    
    Vector
    
    Matrix
    
    S
    
    Matrix
    
    Table
    
    Vector
    
    Table
    
    Universal_genetic_code
    
    NS
    
    Matrix
    
    Table
    
    Vector
    
    Vector
  - Discrete_pd
  - Dna
  - Felsenstein
    
    Alignment
    
    Make
    
    A
    
    Matrix
    
    Table
    
    Vector
    
    Align
    
    E
  - Fitch
  - ID_monad
  - Iupac_nucleotide
    
    Matrix
    
    Table
    
    Vector
  - Linear_algebra
    
    Matrix
    
    S
    
    Matrix
    
    Vector
    
    Vector
  - Linear_algebra_tools
    
    Lacaml
    
    Mat
    
    Vec
  - List1
  - MCMC
    
    M
    
    Alignment
    
    Felsenstein
  - MG94
    
    NSCodon_rate_matrix
  - Mutsel
    
    NSCodon_rate_matrix
  - Nelder_mead
  - Newick
    
    Tree_repr
  - Newick_ast
  - Newick_lexer
  - Newick_parser
    
    Incremental
    
    MenhirInterpreter
  - Newick_parser_errors
  - Nucleotide
    
    Matrix
    
    Table
    
    Vector
  - Nucleotide_process
    
    Random
  - Phylip
  - Phylo_ctmc
    
    Ambiguous
    
    Path_sampler
    
    SV
    
    Uniformized_process
  - Phylogenetic_tree
  - Rate_matrix
    
    Amino_acid
    
    Make
    
    A
    
    Matrix
    
    Table
    
    Vector
    
    Nucleotide
    
    S
  - Rejection_sampling
    
    Make
    
    Align
  - Seq
    
    Base
    
    DNA
    
    Make
    
    B
    
    Make_list
    
    B
    
    S
  - Sequence_generation
    
    Base
    
    Make
    
    A
    
    Matrix
    
    Table
    
    Vector
    
    Align
    
    E
    
    Seq
    
    Sequence
  - Sequence_simulator
    
    Alphabet
    
    Vector
    
    Make
    
    A
    
    Vector
  - Sigs
    
    ALIGNMENT
    
    BASE
    
    EVOL_MODEL
    
    SEQUENCE
  - Simulator
    
    Branch_info
    
    Make
    
    A
    
    Matrix
    
    Table
    
    Vector
    
    BI
    
    NSCodon
    
    BI
  - Site_evolution_model
    
    Diagonalizable_rate_matrix
    
    JC69
    
    JC69_numerical
    
    K80
    
    K80_numerical
    
    Make
    
    A
    
    Matrix
    
    Table
    
    Vector
    
    M
    
    Make_diag
    
    A
    
    Matrix
    
    Table
    
    Vector
    
    M
    
    Nucleotide_S_with_reduction
    
    Rate_matrix
    
    S
    
    S_with_reduction
  - Stat_tools
  - TKF91
    
    Make_simulator
    
    A
    
    Matrix
    
    Table
    
    Vector
    
    BI
  - Tree
  - Utils
  - Wag
  - Zipper

Legend:
Library
Module
Module type
Parameter
Class
Class type

A single DNA base

include Alphabet.S_int

include Alphabet.S
  with type t = private int
   and type vector = private Linear_algebra.vec
   and type matrix = private Linear_algebra.mat
   and type 'a table = private 'a array

type t = private int

type vector = private Linear_algebra.vec

type matrix = private Linear_algebra.mat

type 'a table = private 'a array

val equal : t -> t -> bool

val compare : t -> t -> int

val all : t list

val card : int

val to_int : t -> int

val counts : t Core.Sequence.t -> int table

module Table : sig ... end

module Vector : sig ... end

val flat_profile : unit -> vector

val random_profile : Gsl.Rng.t -> float -> vector

module Matrix : sig ... end

val (.%()) : vector -> t -> float

val (.%()<-) : vector -> t -> float -> unit

val (.%{}) : matrix -> (t * t) -> float

val (.%{}<-) : matrix -> (t * t) -> float -> unit

val of_int : int -> t option

val of_int_exn : int -> t

val a : t

The base 'A'.

val c : t

The base 'C'.

val g : t

The base 'G'.

val t : t

The base 'T'.

val of_char_exn : Char.t -> t

Creates a DNA base from a char (case insensitive). Raises invalid_arg in case of incorrect char parameter.

val to_char : t -> Char.t

Returns a single capital character representing the base.

val transversion : t -> t -> bool

transversion x y is true if x and y belong to different purine/pyrimidine groups.

type repr =

| A
| C
| G
| T

val inspect : t -> repr

Returns the representation of a DNA base as a variant type. The representation can be 'A', 'C', 'G', or 'T'.