On the methodological weakness of 'the effective number of codons': a reply to Marashi and Najafabadi

In a recent publication [Biochem. Biophys. Res. Commun. 317 (2004) 957] it was proposed that the 'effective number of codons' (Nc) in a gene should be calculated by summing the individual amino acid Nc's using rounding whenever the codon homozygosities are lower than the reciprocal value of the number of members of the synonymous families. This led Marashi and Najafabadi to examine the consequences of individual re-adjustment when comparing observed Nc with the expected Nc under assumptions of no selection, and C=G and A=T [Biochem. Biophys. Res. Commun. 324 (2004) 1]. Clearly, the present methodology has some weaknesses; in this work, I discuss these in relation to the observations by Marashi and Najafabadi, and finally an alternative method for the calculation of Nc is introduced with the purpose of eliminating the need for re-adjustments.