Contents

• 1 Installing Ordalie
  • 1.1 Requirements
  • 1.2 Installation
  
  
• 2 Introduction
  • 2.1 Context
  • 2.2 Ordalie
  
  
• 3 Ordalie Basics
  • 3.1 Alignments
  • 3.2 Snapshots
  • 3.3 Sequences names
  • 3.4 Conventions
  • 3.5 The Main Window
  • 3.6 Features
  
  
• 4 Ordalie Tools
  • 4.1 Snapshot Overview
  • 4.2 Editor
  • 4.3 The Identity tool
  • 4.4 The Search motif tool
  • 4.5 The Clustering tool
  • 4.6 The Tree tool
  • 4.7 The Conservation tool
  • 4.8 The Superposition tool
  • 4.9 The 3D Viewer tool
  • 4.10 The Features Editor
  • 4.11 The Features Summary
  • 4.12 The Annotation tool
  • 4.13 Barcode
  
  
• 5 Menus Description
  • 5.1 The File Menu
  • 5.2 The Edit Menu
  • 5.3 The View Menu
  • 5.4 The Sequence Menu
  • 5.5 The Alignment Menu
  • 5.6 The Structure Menu
  • 5.7 The "?" Menu
  • 5.8 Help
  
  
• 6 Appendix
  • 6.1 The Ordalie database scheme
  • 6.2 The FindPatterns syntax
  • 6.3 The Vector Norm scoring method
  • 6.4 The Feature File Format
  • 6.5 The superposition algorithm
  • 6.6 The command line options
  
  
• Bibliography