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The past decade has seen the emergence of a new field of scientific inquiry at the intersection of phylogenetics and genomics: phylogenomics. In Phylogenomics, leading researchers contribute cutting-edge protocols and resources in order to describe many of the molecular methods and bioinformatics tools that have brought this field to fruition. The chapters cover topics such as the use of cytogenetic methods for characterizing the genomes of different species and BAC clone isolation, sequencing and analysis. Written in the highly successful Methods in Molecular Biology series format, each subject is covered with a brief introduction, readily reproducible protocols, a list of the necessary materials and reagents, and tips for troubleshooting and avoiding known pitfalls. Comprehensive and up-to-date, Phylogenomics is a resource that will invigorate the comparative analysis of genomes across all branches of the tree of life.