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Table of Contents
Documentation of
qod
and
qodgui
version 1.0.2
1 How to Read This Manual
CeCILL FREE SOFTWARE LICENSE AGREEMENT
Notice
Preamble
Article 1 - DEFINITIONS
Article 2 - PURPOSE
Article 3 - ACCEPTANCE
Article 4 - EFFECTIVE DATE AND TERM
Article 5 - SCOPE OF RIGHTS GRANTED
Article 6 - INTELLECTUAL PROPERTY
Article 7 - RELATED SERVICES
Article 8 - LIABILITY
Article 9 - WARRANTY
Article 10 - TERMINATION
Article 11 - MISCELLANEOUS
Article 12 - NEW VERSIONS OF THE AGREEMENT
Article 13 - GOVERNING LAW AND JURISDICTION
2 Overview
2.1 Presentation
2.2 Advantages of
qod
2.3 Maximal Common Intervals and Segmentation of the Central Genome
2.4 Partitionning the Central Genome
2.5 Transfering Annotations
3 How to run
qod
and
qodgui
3.1 How to run
qod
3.2 How to run
qodgui
3.2.1 Setting a shortcut on your desktop
3.2.2 Command line invokation
4 Sample Output
4.1
qod
invocation with the
--help
option
4.2
qod
invocation with the
--full-version
option
4.3 Simple
qod
invocation on biological data
4.4 More complicated
qod
invocation on biological data
5 How to use the graphical interface
5.1 Interacting with
qodgui
interface
5.2 Configuring
qodgui
5.3 Visualizing the output
5.3.1 Text structuration
5.3.2 Keyword search facility
5.3.3 Diagrams representations
5.4 Menu description
5.4.1 File menu
5.4.2 Edit menu
5.4.3 View menu
5.4.4 Help menu
6 External Resources
7 Reporting Bugs
Concept Index