This volume describes the foundations of phylogenomic analysis, bioinformatic resources, methodologies supporting the interface of genomic biology, and recent developments in phylogenomic analyses.  Chapters guide readers through advances and challenges in the analysis of shallow and deep evolutionary processes with the retrodiction paradigm, analysis of viruses in pandemics, building a tree of life describing the organismal diversity of our planet, or mining k-mers or structural domains to understand the origin and evolution of proteins and proteomes. Written in the highly successful Methods in Molecular Biology series format, the chapters include brief introductions to the material, lists of necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and a Notes section which highlights tips on troubleshooting and avoiding known pitfalls.  Authoritative and cutting-edge, Evolutionary Genomics: Methods and Protocols aims to be comprehensive guide for researchers in the field.