package phylogenetics

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package phylogenetics
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.