package phylogenetics

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Types
Creation / conversion
Constructors / object manipulation
Observation
Movement
Pretty printing

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
  - Bpp_model
  - 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
  - Newick_ast
  - Newick_lexer
  - Newick_parser
    
    Incremental
    
    MenhirInterpreter
  - Newick_parser_errors
  - Nucleotide
    
    Matrix
    
    Table
    
    Vector
  - Phylip
  - Phylo_ctmc
  - 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

Zipper type for fast operations on large phylogenetic trees.

Types

type t

type branch = float * Phylogenetic_tree.t

type direction =

| Dir0
| Dir1
| Dir2

type location_type =

| LocLeaf
| LocBranch
| LocNode

type oriented_zipper

Creation / conversion

val of_tree : Phylogenetic_tree.t -> t

val of_tree_dir : Phylogenetic_tree.t -> oriented_zipper

val to_tree : t -> Phylogenetic_tree.t

val orient : t -> direction -> oriented_zipper

val unorient : oriented_zipper -> t

Constructors / object manipulation

val string_of_dir : direction -> string

val dir_of_string : string -> direction

Observation

val equal : t -> t -> bool

val get_branch : t -> direction -> branch

val get_index : t -> Sigs.index

val get_length : t -> direction -> float

val get_tree : t -> direction -> Phylogenetic_tree.t

val length_left : oriented_zipper -> float

val length_right : oriented_zipper -> float

val location : t -> location_type

Movement

val goto : t -> int -> t

val init_routing : t -> t

val left : oriented_zipper -> direction

val move : t -> direction -> t

val move_left : oriented_zipper -> oriented_zipper

val move_right : oriented_zipper -> oriented_zipper

val random_node : t -> t

val right : oriented_zipper -> direction

val slide : t -> direction -> float -> t

Pretty printing

val pp : Stdlib.Format.formatter -> t -> unit

val pp_fancy : Stdlib.Format.formatter -> t -> unit

val print : t -> unit

val print_fancy : t -> unit