In the first part of this book we give an introduction to basic concepts from graph theory and systematics (Chapter 1). We briefly discuss the problem of aligning molecular sequences (Chapter 2) and give a more detailed introduction to the computation of phylogenetic trees from aligned sequences and distances (Chapter 3). Finally, we give a brief introduction to the computation of phylogenetic networks, which also serves as an overview for the material presented in the second and third parts of the book (Chapter 4).

Chapters 2 and 3 are provided for the sake of completeness and reference. They can be skipped by readers who have a basic knowledge of phylogenetic analysis.