As a standard method for scatter plot visualization of codon usage data, researchers mostly resort to the so-called correspondence analysis (CA) which has originally been developed for the analysis of contingency tables [5]. From the original formulation it is not completely clear how CA applies to codon counts. Because different preprocessing and normalization schemes have been proposed, the use of CA in codon usage studies has not been without controversy [6]. Nevertheless, CA has been applied for the analysis of many bacterial genomes, including those of Escherichia coli [1,3], Bacillus subtilis [4,7,8], Borrelia burgdorferi [9,10], Chlamydia trachomatis [11], Mycoplasma genitalium [12], Helicobacter pylori [13] and Pseudomonas aeruginosa [14].