Module Cgr


module Cgr: sig .. end
MyCGR: Collection of modules to manipulate DNA sequences, and compute and use the Chaos Game Representation.


Base


module Types: Cgr_types
Types for sequences, CGR-trees (Digital Search Trees based on CGR) and the type of the common parameter module for computing CGR on segment, square, ...
module Constants: Cgr_constants
Constants.
module Global: Cgr_global
Global variables.
module Misc: Cgr_misc
Miscellaneous functions.
module Config: Cgr_config
Configuration values need by some tools, like meta_cenac.x.
module Seq: Cgr_seq
Manipulating DNA sequences (reading, writing, generating from IID or Markov models, ...
module Entrez: Cgr_entrez
Retrieving sequences from Entrez.

Utilities to do some mathematics and statistics


module Quantiles: Cgr_quantiles
Predefined quantiles for Chi2 distribution.
module Extmath: Cgr_extmath
Using well-known distributions quantiles and probabilities with the help of of external tool (Octave of Scilab).

Manipulating matrices for results and distances


module Matrix: Cgr_matrix
module Distances: Cgr_distances

Generating random sequences


module Cenac_random: Cgr_cenac_random
Various random generators
module Random_seq: Cgr_random_seq
Generating random sequences

Different representations for the CGR



Generic computation using barycenters


module Generic: Cgr_generic

On segment


module Segment: Cgr_segment
To compute CGR on segment.
module Binary: Cgr_binary
To compute CGR on segment with only two elements.

On square


module Square_types: Cgr_square_types
module Square_base: Cgr_square_base
module Square: Cgr_square

On tetrahedron


module Space: Cgr_space
Various functions to compute coordinates in space.
module Tetra: Cgr_tetra
CGR on tetrahedron

The Cenac method


module Cenac: Cgr_cenac
Main module to compute CGR and work on it.
module Simu: Cgr_simu
module Pearson: Cgr_pearson
module Latex: Cgr_latex
Printing LaTeX code from the results of distances computations.
module Neighbor: Cgr_neighbor
Creating tree with the Neighbor-joining clustering method.
module Cenac_options: Cgr_cenac_options
Module defining options used to various tools.
module Cenac_main: Cgr_cenac_main
Main modules for various Cenac tools.
module Cenac_zones: Cgr_cenac_zones
Main module of the Cenac_???_zones tools.
module Cenac_test: Cgr_cenac_test
Main module of the Cenac tests tools.
module Run_tests: Cgr_run_tests
Running tests.
module Test_frequency: Cgr_test_frequency
Tests based on frequencies.
module Repartition: Cgr_repartition
Creating and drawing repartitions (using OCaml-gnuplot).

CGR-trees


module Tree: Cgr_tree
Digital Search Trees based on CGR.

Storing in a MySQL database


module Db: Cgr_db
module Dbbase: Cgr_dbbase
module Dbtree: Cgr_dbtree
module Dbseqs: Cgr_dbseqs
module Dbzones: Cgr_dbzones

Additional


module Eqn: Cgr_eqn
Solving non-linear equations of degree 2, 3 or 4.