**Abstract**

The ratios of amino acids to the total amino acids deduced from the complete genome and those of nucleotides to the total nucleotides in the genome are useful indexes to characterize various large genomes among different species from bacteria to *Homo sapiens*. These indexes are not only independent of species but also of genome size. Using these indexes, the following results were obtained: (1) primitive life forms appeared to have similar amino acid compositions to present day organisms; (2) cellular amino acid compositions that are similar among various species and between whole cells and complete genomes; (3) genome structure that is homogeneously constructed from putative small units encoding proteins of similar amino acid compositions, followed by synchronous mutations over the genome; (4) all organisms can be classified into two groups, "GC-rich" and "AT-rich," based on their nucleotide contents, or "terrestrial" and "aquatic vertebrates" based on natural selection by cluster analyses using amino acid contents as the traits; and (5) evolution based on nucleotide content alterations can be expressed by definitive equations. Thus, the ratios of amino acids or nucleotides to their total contents are useful indexes for characterizing genomes, regardless of species differences and genome sizes. The two normalized nucleotide contents are universally expressed regression line.

**Keywords:** genome, mitochondria, codons, Chargaff's parity rules, cluster analysis, normalization, phylogenetic trees, evolution
