The idea for The Phylogenetic Handbook was conceived during an early edition of the Workshop on Virus Evolution and Molecular Epidemiology. The rationale was simple: to collect the information being taught in the workshop and turn it into a comprehensive, yet simply written textbook with a strong practical component. Marco and Annemie took up this challenge, and, with the help of many experts in the field, successfully produced the First Edition in 2003. The resulting text was an excellent primer for anyone taking their first computational steps into evolutionary biology, and, on a personal note, inspired me to try out many of the techniques introduced by the book in my own research. It was therefore a great pleasure to join in the collaboration for the Second Edition of The Phylogenetic Handbook.

Computational molecular biology is a fast-evolving field in which new techniques are constantly emerging. A book with a strong focus on the software side of phylogenetics will therefore rapidly grow a need for updating. In this Second Edition, we hope to have satisfied this need to a large extent. We also took the opportunity to provide a structure that groups different types of sequence analyses according to the evolutionary hypothesis they focus on. Evolutionary biology has matured into a fully quantitative discipline, with phylogenies themselves having evolved from classification tools to central models in quantifying underlying evolutionary and population genetic processes.