Goldman and Yang [2] proposed a codon-based model for the evolution of protein-coding DNA sequences using a Markov process to describe substitutions between codons. They used codon level information to model synonymous and asynonymous nucleotide substitution applicable to homologous sequences with no insertion/deletion gaps or with gaps removed. A 61661 matrix of codon substitution rates (excluding the three stop codons) is used, assuming that mutations occur at the three codon positions independently and only single-nucleotide substitutions are permitted to occur at any instant. Using several constraints and refinements on the nucleotide substitution rates, the transition/ transversion bias and amino acid differences, they show that their codon based model gives better phylogenies than simple nucleotide substitution model. However, the possible patterns arising from this model is very large and computationally very slow requiring Monte Carlo simulations, maximum likelihood methods and other approximations to arrive at quantitative results. While the model is useful for pairwise distance measures and for phylogenies, a relationship defining base composition in a DNA sequence is not clearly realised.