MyCGR
What is MyCGR ?
MyCGR is an Objective-Caml library and a collection of tools to use the Chaos Game Representation on DNA sequences.

This software is experimental. It was developed during the thesis of Peggy Cénac and can be used to run the simulations and experiments described in this thesis. This software (including the source code) is made available to allow its use and the addition of functionalities within the framework of other research.

News

Source code is available (22 Jun 2006 15:10:00 +0000)
Version 0.98 is available for download and the development site is now public.

Site on line (18 Apr 2006 15:30:00 +0000)
The MyCGR site is now in line. The software will be available soon.

Installation
The instructions to download and install the MyCGR software are on this page.
Documentation

Library Reference: reference documentation on the Cgr library, an Objective-Caml library included in MyCGR. This library offers modules to manipulate DNA sequences, compute CGR, perform tests on structures of sequences, compute distances between species, ...

Overview of tools: a nonexhaustive list of the programs included in MyCGR, with their main functionalities.

First steps: indications to start to use MyCGR.

Results

Some results of simulations carried out with MyCGR are available on this site:

References
Peggy Cénac: Étude statistique de séquences biologiques et convergence presque sûre de martingales
This is the thesis these tools were developed for. One can find there the definitions, constructions and methods implemented in MyCGR.
Peggy Cénac: Test on the structure of biological sequences via Chaos Game Representation
Statistical Applications in Genetics and Molecular Biology, Volume 5, 2005, article 27.
Peggy Cénac, Guy Fayolle and Jean-Marc Lasgouttes: Dynamical systems in the analysis of biological sequences.
Technical report 5351, INRIA, Octobre 2004.
License

This software is distributed under the Cecill license.
Release 0.98 was registered at the Agence de Protection des Programmes (APP) with number IDDN.FR.001.230010.000.S.P.2006.000.10000.

Authors
Peggy Cénac
Maxence Guesdon
[peggy DOT cenac AT inria DOT fr]
[maxence DOT guesdon AT inria DOT fr]