package phylogenetics

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package phylogenetics
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Module PhylogeneticsSource

Sourcemodule Alignment : sig ... end

A representation for sequence alignments

Sourcemodule Alphabet : sig ... end

Integer-based representation of sequence alphabets

Sourcemodule Amino_acid : sig ... end

Integer-based representation for amino acids

Sourcemodule Birth_death : sig ... end

Simulation for birth-death models

Sourcemodule Bppsuite : sig ... end

Utility functions to call programs from the Bio++ library

Sourcemodule Codon : sig ... end

Abstract representations of codons and genetic codes

Sourcemodule Discrete_pd : sig ... end

Updatable discrete probability distribution

Sourcemodule Dna : sig ... end

Strings that represent valid DNA sequences

Sourcemodule Felsenstein : sig ... end

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

Sourcemodule Fitch : sig ... end

Phylogenetic inference by parcimony

Sourcemodule ID_monad : sig ... end

A state monad to generate integer identifiers

Sourcemodule Iupac_nucleotide : sig ... end

Nucleotide IUPAC symbol

Sourcemodule Linear_algebra : sig ... end

This modules wraps linear algebra functions

Sourcemodule Linear_algebra_tools : sig ... end

Deprecated, see Linear_algebra. This modules wraps linear algebra functions (from Lacaml) and provide a few completely new functions (such as exponentiation)

Sourcemodule List1 : sig ... end

Lists with at least one element

Sourcemodule MCMC : sig ... end

Deprecated. A simple implementation of the Monte Carlo Markov Chain algorithm

Sourcemodule MG94 : sig ... end

Codon rate matrix from Muse and Gaut 94

Sourcemodule Mutsel : sig ... end

Mutation-selection model for codons

Sourcemodule Nelder_mead : sig ... end

An implementation of Nelder-Mead algorithm for function optimization

Sourcemodule Newick : sig ... end
Sourcemodule Newick_ast : sig ... end
Sourcemodule Newick_lexer : sig ... end
Sourcemodule Newick_parser : sig ... end
Sourcemodule Newick_parser_errors : sig ... end
Sourcemodule Nucleotide : sig ... end

A single DNA base

Sourcemodule Nucleotide_process : sig ... end

A representation of classical parametric processes on nucleotides

Sourcemodule Phylip : sig ... end

Parsing for the PHYLIP format

Sourcemodule Phylo_ctmc : sig ... end

Likelihood calculations for continuous-time Markov chain along a tree

Sourcemodule Phylogenetic_tree : sig ... end

Module for phylogenetic trees.

Sourcemodule Rate_matrix : sig ... end

Continuous Time Markov Chain rate matrix

Sourcemodule Rejection_sampling : sig ... end

Deprecated. Utility functions for rejection sampling

Sourcemodule Seq : sig ... end

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

Sourcemodule Sequence_generation : sig ... end

Deprecated. Simulation functions for sequences

Sourcemodule Sequence_simulator : sig ... end

Functions to simulate sequences

Sourcemodule Sigs : sig ... end

Compilation of module signatures used elsewhere.

Sourcemodule Simulator : sig ... end
Sourcemodule Site_evolution_model : sig ... end

Deprecated. 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.

Sourcemodule Stat_tools : sig ... end

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

Sourcemodule TKF91 : sig ... end

Simulator for alignments with indels under the model by Thorne, Kishino and Felsenstein.

Sourcemodule Tree : sig ... end

Tree structure with annotations on leaves, internal nodes and branches.

Sourcemodule Utils : sig ... end
Sourcemodule Wag : sig ... end

WAG matrix parser

Sourcemodule Zipper : sig ... end

Zipper type for fast operations on large phylogenetic trees.