package phylogenetics

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in-package search v0.2.0

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

type ('n, 'l, 'b) t =

| Node of {
1. data : 'n;
2. branches : ('n, 'l, 'b) branch List1.t;
}
| Leaf of 'l

and ('n, 'l, 'b) branch =

| Branch of {
1. data : 'b;
2. tip : ('n, 'l, 'b) t;
}

val sexp_of_t : 
  ('n -> Sexplib0.Sexp.t) ->
  ('l -> Sexplib0.Sexp.t) ->
  ('b -> Sexplib0.Sexp.t) ->
  ('n, 'l, 'b) t ->
  Sexplib0.Sexp.t

val sexp_of_branch : 
  ('n -> Sexplib0.Sexp.t) ->
  ('l -> Sexplib0.Sexp.t) ->
  ('b -> Sexplib0.Sexp.t) ->
  ('n, 'l, 'b) branch ->
  Sexplib0.Sexp.t

val t_of_sexp : 
  (Sexplib0.Sexp.t -> 'n) ->
  (Sexplib0.Sexp.t -> 'l) ->
  (Sexplib0.Sexp.t -> 'b) ->
  Sexplib0.Sexp.t ->
  ('n, 'l, 'b) t

val branch_of_sexp : 
  (Sexplib0.Sexp.t -> 'n) ->
  (Sexplib0.Sexp.t -> 'l) ->
  (Sexplib0.Sexp.t -> 'b) ->
  Sexplib0.Sexp.t ->
  ('n, 'l, 'b) branch

val leaf : 'l -> (_, 'l, 'b) t

val node : 'a -> ('a, 'b, 'c) branch List1.t -> ('a, 'b, 'c) t

val binary_node : 
  'a ->
  ('a, 'b, 'c) branch ->
  ('a, 'b, 'c) branch ->
  ('a, 'b, 'c) t

val branch : 'c -> ('a, 'b, 'c) t -> ('a, 'b, 'c) branch

val data : ('a, 'a, _) t -> 'a

val to_printbox : 
  ?node:('n -> string) ->
  ?leaf:('l -> string) ->
  ?branch:('b -> string option) ->
  ('n, 'l, 'b) t ->
  PrintBox.t

val map : 
  ('a, 'b, 'c) t ->
  node:('a -> 'd) ->
  leaf:('b -> 'e) ->
  branch:('c -> 'f) ->
  ('d, 'e, 'f) t

val map2_exn : 
  ('a, 'b, 'c) t ->
  ('d, 'e, 'f) t ->
  node:('a -> 'd -> 'x) ->
  leaf:('b -> 'e -> 'y) ->
  branch:('c -> 'f -> 'z) ->
  ('x, 'y, 'z) t

val map_branch2_exn : 
  ('a, 'b, 'c) branch ->
  ('d, 'e, 'f) branch ->
  node:('a -> 'd -> 'x) ->
  leaf:('b -> 'e -> 'y) ->
  branch:('c -> 'f -> 'z) ->
  ('x, 'y, 'z) branch

val propagate : 
  ('n1, 'l1, 'b1) t ->
  init:'s ->
  node:('s -> 'n1 -> 's * 'n2) ->
  leaf:('s -> 'l1 -> 'l2) ->
  branch:('s -> 'b1 -> 's * 'b2) ->
  ('n2, 'l2, 'b2) t

val prefix_traversal : 
  ('n, 'l, 'b) t ->
  init:'c ->
  node:('c -> 'n -> 'c) ->
  leaf:('c -> 'l -> 'c) ->
  branch:('c -> 'b -> 'c) ->
  'c

val leaves : (_, 'l, _) t -> 'l list

val fold_leaves : (_, 'l, _) t -> init:'a -> f:('a -> 'l -> 'a) -> 'a

val unfold : 
  ('n, 'l, 'b) t ->
  init:'a ->
  branch:('e -> 'b -> 'a * 'bb) ->
  leaf:('a -> 'l -> 'e * 'll) ->
  node:('a -> 'n -> 'e * 'nn) ->
  ('nn, 'll, 'bb) t

val leafset_generated_subtree : 
  ('n, 'l, 'b) t ->
  ('l -> string option) ->
  string list ->
  ('n, 'l, 'b) t option

leafset_generated_subtree t f xs returns the maximal subtree of t whose leaves all return a string in xs when applied to f if it exists (and None otherwise)

val simplify_node_with_single_child : 
  merge_branch_data:('b list -> 'b) ->
  ('n, 'l, 'b) t ->
  ('n, 'l, 'b) t