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1 Obtaining and Installing
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Contents
1 Obtaining and Installing
1.1 Requirements
2 Introduction
2.1 Context
2.2 Ordalie
3 Ordalie Basics
3.1 Alignments and sequences names
3.2 The Main Window
3.3 Features
3.4 Tools
3.5 Conventions
4 Sequence Tools
4.1 The Identity tool
4.2 The Search motif tool
4.3 Sequence information browser and editor
4.4 VRP
4.5 Feature Editor
5 Alignment Tools
5.1 Snapshot Overview
5.2 Editor
5.3 Clusters
5.4 The Tree tool
5.5 The Conservation tool
5.6 Superposition tool
5.7 3D Viewer
5.8 The Features Summary
5.9 Barcode alignment
6 Menus Description
6.1 The File Menu
6.2 The Edit Menu
6.3 The View Menu
6.4 The Sequence Menu
6.5 The Alignment Menu
6.6 The Structure Menu
6.7 The "?" Menu
6.8 help
7 Appendix
7.1 The command line options
7.2 The Ordalie database scheme
7.3 The Vector Norm scoring method
7.4 The Feature File Format
7.5 The superposition algorithm
Bibliography