The past decade has seen the emergence of a new field of scientific inquiry at the intersection of phylogenetics and genomics: phylogenomics. From one perspective, phylogenomics is defined as the use of large genomic data sets to aid in difficult phylogeny problems. Alternatively, phylogenomics may be described as the use of phylogeny and comparative analysis to infer processes of genome evolution. Regardless of how one defines the field, the two app- cations are intertwined. This volume is a collection of protocols and resources compiled by leading researchers in the field and describes many of the molecular methods and bioinformatics tools that have brought this field to fruition in recent years. Several chapters in this volume highlight the use of cytogenetic methods for characterizing the genomes of different species. Fluorescent in-situ hybridization (FISH) is a powerful tool for establishing chromosome homologies between divergent species. The broadest of these techniques is chromosome painting, which in recent years has been performed on members of nearly every order of eutherian mammals, and across marsupial and avian orders. FISH mapping of single copy clones (e. g. cDNAs, fosmids, and BACS) can provide ordered gene mapping from megabase-pair resolution on metaphase preparations down to exquisite kilobase-pair resolution detail with extended-fiber techniques. Other chapters highlight the construction and development of radiation-hybrid (RH) maps, now fueled by thousands of markers from either large scale BAC-end sequencing projects or survey-sequenced genomes.