package phylogenetics

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phylogenetics
- Phylogenetics
  - Alignment
    
    Make
    
    S
  - 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
    
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    Vector
    
    Matrix
    
    S
    
    Matrix
    
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    Vector
    
    Table
    
    Universal_genetic_code
    
    NS
    
    Matrix
    
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    Vector
    
    Vector
  - Discrete_pd
  - Dna
  - Felsenstein
    
    Alignment
    
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    A
    
    Matrix
    
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    Align
    
    E
  - Fitch
  - ID_monad
  - Iupac_nucleotide
    
    Matrix
    
    Table
    
    Vector
  - Linear_algebra
    
    Matrix
    
    S
    
    Matrix
    
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    Vector
  - Linear_algebra_tools
    
    Lacaml
    
    Mat
    
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  - List1
  - MCMC
    
    M
    
    Alignment
    
    Felsenstein
  - Mutsel
    
    NSCodon_rate_matrix
  - Nelder_mead
  - Newick
  - Newick_ast
  - Newick_lexer
  - Newick_parser
    
    Incremental
    
    MenhirInterpreter
  - Newick_parser_errors
  - Nucleotide
    
    Matrix
    
    Table
    
    Vector
  - Nucleotide_process
    
    Random
  - Phylip
  - Phylo_ctmc
  - Phylogenetic_tree
  - Rate_matrix
    
    Amino_acid
    
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    A
    
    Matrix
    
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    Nucleotide
    
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  - Rejection_sampling
    
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    Sequence
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    ALIGNMENT
    
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    BI
    
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  - Site_evolution_model
    
    Diagonalizable_rate_matrix
    
    JC69
    
    JC69_numerical
    
    K80
    
    K80_numerical
    
    Make
    
    A
    
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    M
    
    Make_diag
    
    A
    
    Matrix
    
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    M
    
    Nucleotide_S_with_reduction
    
    Rate_matrix
    
    S
    
    S_with_reduction
  - Stat_tools
  - TKF91
    
    Make_simulator
    
    A
    
    Matrix
    
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    BI
  - Tree
  - Utils
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Legend:
Library
Module
Module type
Parameter
Class
Class type

A representation of classical parametric processes on nucleotides

type t =

| JC69
| K80 of float
| HKY85 of {
1. equilibrium_frequencies : Nucleotide.vector;
2. transition_rate : float;
3. transversion_rate : float;
}
| GTR of {
1. equilibrium_frequencies : Nucleotide.vector;
2. exchangeabilities : Linear_algebra.vec;
}

val rate_matrix : t -> Rate_matrix.Nucleotide.t

val stationary_distribution : t -> Nucleotide.vector

module Random : sig ... end