Two-dimensional cluster analysis of differential codon preferences for tCAI and dCAI. The differences in relative adaptiveness of each codon (wij for tCAI minus wij for dCAI) for each Genbank entry were clustered into two dimensions, one clustering codons and the other clustering Genbank entries. The clustering was performed as a hierarchical cluster analysis using Euclidian distances and complete linkage. Codons preferred relatively more by dCAI are red, whereas codons preferred relatively more by tCAI are green. Equal preference is indicated by white. (a) Entire dendrogram. The five major regions are indicated and microbial names are replaced by a color bar reflecting each microbe's phylum. (b) Zoom of the third and fourth regions. Weights not considered: start codon 'ATG' and stop codons 'TGA', 'TAG' and 'TAA'. dCAI, dominant codon adaptation index; tCAI, translational codon adaptation index.