The past decade has seen the emergence of a new field of scientific inquiry at the intersection of phylogenetics and genomics: phylogenomics. This volume is a collection of protocols and resources compiled by leading researchers in the field. It describes many of the molecular methods and bioinformatics tools that have brought this field to fruition in recent years. It contains step-by-step instructions that ensure successful results, and provides tricks of the trade and notes on troubleshooting and avoiding known pitfalls.