In order to derive a suitable low-dimensional point representation of genes we apply classical multidimensional scaling (see e.g. [19]) to the above similarities. The objective is to find a two-dimensional point configuration with interpoint distances reflecting the codon usage similarities of the corresponding genes. To perform classical scaling based on similarities we first transform the similarity matrix S into a positive semi-definite matrix C by subtracting the smallest eigenvalue λmin of S from all of its diagonal elements: