package phylogenetics

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phylogenetics
- Phylogenetics
  - Alignment
    
    Fasta
    
    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
    
    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
  - 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
    
    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
    
    Make
    
    A
  - 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 representation for sequence alignments

The following invariants are maintained:

the alignment is non-empty
all sequences have the same length

type t

val nrows : t -> int

val ncols : t -> int

val description : t -> int -> string

val sequence : t -> int -> string

type error = [

| `Empty_alignment
| `Unequal_sequence_lengths

]

val pp_error : 
  Ppx_deriving_runtime.Format.formatter ->
  error ->
  Ppx_deriving_runtime.unit

val show_error : error -> Ppx_deriving_runtime.string

val map : 
  t ->
  f:(description:string -> sequence:string -> string * string) ->
  (t, [> `Unequal_sequence_lengths ]) Stdlib.result

val array_mapi : 
  t ->
  f:(int -> description:string -> sequence:string -> 'a) ->
  'a array

val fold : 
  t ->
  init:'a ->
  f:('a -> description:string -> sequence:string -> 'a) ->
  'a

val find_sequence : t -> string -> string option

type parsing_error = [

| `Fasta_parser_error of string
| error

]

val pp_parsing_error : 
  Ppx_deriving_runtime.Format.formatter ->
  parsing_error ->
  Ppx_deriving_runtime.unit

val show_parsing_error : parsing_error -> Ppx_deriving_runtime.string

val of_assoc_list : (string * string) list -> (t, [> error ]) Stdlib.result

module Fasta : sig ... end

val indel_free_columns : t -> bool array

val residues : t -> column:int -> Core.Char.Set.t

val number_of_residues_per_column_stats : t -> (int * int) list

val composition : t -> (Stdlib.Char.t * float) list

val constant_site : t -> int -> bool

module Make
  (S : Seq.S) : 
  Sigs.ALIGNMENT with type base = S.base and type sequence = S.t

Legacy code: provides a functor to build from SEQUENCE modules.