Recently, Elhaik et al. [Elhaik, E., Graur, D., Josic, K., 2008. ‘Genome order index’ should not be used for defining compositional constraints in nucleotide sequences. Comp. Biol. Chem. 32, 147] commented on the genome order index, which is defined as S = a2 + c2 + g2 + t2 where a, c, g and t denote corresponding base frequencies. They claimed that (1) “S < 1/3 is in fact a mathematical property that is always true”, and (2) “S is strictly equivalent to and derivable from the Shannon H function”. The first claim is apparently wrong: for instance, when a = c =0.5, g = t =0, S = 0.5 > 1/3. The second claim is also incorrect because S and H are different special cases of the α-order entropy, having different functional forms that are neither strictly derivable from nor equivalent to each other. Therefore, the conclusions made in their comments are wrong.