The evolutionary conservation of RSCU (A) and RDCU (B) in the genomes studied. The branch lengths characterize the correlation of RSCU or RDCU usage between two organisms – the higher the correlation, the shorter the branch. In general, the branch lengths of the RSCU tree are shorter than those of the RDCU tree, showing stronger similarity of codon usage than codon pair usage between different organisms. Bacilli, gamma-proteobacteria and alpha-proteobacteria form very similar clusters on both trees. Eukaryotes, which are spread around the RSCU tree, are all clustered together in the RDCU tree. For the full names of organisms see [additional file 6].