Certain parts of this book are mathematical or algorithmic in nature, so you will find various `equations and computer programs throughout the book. If these notations are unfamiliar to you, don't panic. To make this book accessible to a general audience, we have included graphical examples and descriptive text along with the equations. The programming examples are written in Perl, one of the most popular programming languages and one that has an especially strong following in bioinformatics. While we could have relied on pseudocode for our examples, using a real language means that you can run the programs on your own computer and edit them as you wish.