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
    
    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
  - Nucleotide_process
    
    Random
  - 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

module Alignment : sig ... end

A representation for sequence alignments

module Alphabet : sig ... end

module Amino_acid : sig ... end

module Birth_death : sig ... end

module Bppsuite : sig ... end

module Codon : sig ... end

module Discrete_pd : sig ... end

module Dna : sig ... end

module Felsenstein : sig ... end

Functions that implement Felsenstein's "pruning" algorithm to compute likelihood of phylogenetic trees with known sequences at leaves.

module Fitch : sig ... end

module ID_monad : sig ... end

A state monad to generate integer identifiers

module Iupac_nucleotide : sig ... end

Nucleotide IUPAC symbol

module Linear_algebra : sig ... end

This modules wraps linear algebra functions

module Linear_algebra_tools : sig ... end

This modules wraps linear algebra functions (from Lacaml) and provide a few completely new functions (such as exponentiation)

module List1 : sig ... end

module MCMC : sig ... end

module Mutsel : sig ... end

https://www.biorxiv.org/content/biorxiv/early/2016/04/30/037689.full.pdf https://academic.oup.com/mbe/article/34/1/204/2656188

module Nelder_mead : sig ... end

An implementation of Nelder-Mead algorithm for function optimization

module Newick : sig ... end

module Newick_ast : sig ... end

module Newick_lexer : sig ... end

module Newick_parser : sig ... end

module Newick_parser_errors : sig ... end

module Nucleotide : sig ... end

A single DNA base

module Nucleotide_process : sig ... end

A representation of classical parametric processes on nucleotides

module Phylip : sig ... end

The original format is described there. This implementation also allows a somewhat more relaxed syntax:

module Phylo_ctmc : sig ... end

module Phylogenetic_tree : sig ... end

Module for phylogenetic trees.

module Rate_matrix : sig ... end

Continuous Time Markov Chain rate matrix

module Rejection_sampling : sig ... end

module Seq : sig ... end

Module for sequences of bases. Provides a functor to build the module for any base module with the BASE signature.

module Sequence_generation : sig ... end

module Sequence_simulator : sig ... end

module Sigs : sig ... end

Compilation of module signatures used elsewhere.

module Simulator : sig ... end

module Site_evolution_model : sig ... end

Compilation of modules implementing evolution models and providing relevant mathematical procedure (eg, exponential of transition matrix); also includes functors to build models from transition matrices.

module Stat_tools : sig ... end

Probability and statistics tools (eg, samplers and distribution handling).

module TKF91 : sig ... end

module Tree : sig ... end

module Utils : sig ... end

module Wag : sig ... end

WAG matrix parser

module Zipper : sig ... end

Zipper type for fast operations on large phylogenetic trees.