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