The genetic code has evolved to enable most amino acids to be encoded by multiple synonymous codons. These codon usage patterns can vary between genes and this provides a basis of comparison for studying the compositional histories and evolution of genomes. Codon usage patterns also tend to be species specific, so they can be used to study the genomic effects of species divergence. In previous work, we developed automated tools for analyzing genomes using codon usage data. In this talk, I will describe these tools and show how they have improved our understanding horizontal gene transfer patterns in Escherichia and Salmonella species. Finally, I will also discuss the some of the benefits and limitations of using codon usage data to characterize the contents of a metagenome.