Establishing the rules of codon usage is of interest with respect to fundamental evolutionary questions (e.g., in horizontal gene transfer, the genomic signature), in gene prediction, in characterizing properties of a given gene, and in classifying gene families. New measures of relative codon biases, dicodon biases, dinucleotide relative abundance distances between codon sites will be set forth. In these terms, comparisons of codon usage between different gene classes for several complete prokaryotic genomes will be discussed. Correlations of codon bias and levels of gene expression (particularly, in E. coli and yeast) will be assessed. Methods for gene clustering by codon usage will be reviewed.