Bio++ Tutorial & Cookbook

Bio++ Tutorial & Cookbook
Julien Dutheil
Sylvain Gaillard
March 31, 20102i
This tutorial aims at providing help for getting started with the Bio++ libraries.
It introduces some of the Bio++ fundamental classes in order to get familiar with the
libraries philosophy. For an exhaustive list of available classes and methods, or get a de-
tailed description of what each class can do, one shouldlook at the class documentation.
Each section in this tutorial works on a detailed example. Each new object instan-
tiated is introduced briefly, and all methods are described.
Prerequisite Users must have a basic knowledge of the C(++) language. An experi-
ence in object programming will help, but is not absolutely required for the first part of
this tutorial.
Organization of this manual This manual starts with a general introduction to
Bio++, and with technical concern on how to install and use the Bio++ libraries on
variousoperatingsystems. Thefirstpartofthismanualthenconsistsin basicutilization
of Bio++. It is split into thematic chapters. Each chapter begins with a working
example, followed by more detailed explanation on the classes introduced.
The second part of the manual will consist of several recipes on how to perform
various kinds of analyses.iiContents
1 Introduction 1
1.1 You probably want to know... . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.1.1 Whether Bio++ is a C++ port of BioPerl, BioJava or BioPython? 2
1.1.2 What are the legal limitations when using ...