Several papers [1, 4, 5, 7, [13] [14] [15] [16] 18] have been dedicated towards the study of selection on viral genomes, in particular focusing attention on the evolutionary behaviour of overlapping reading frames. These are a feature common to viruses, where due to the three periodicity of the genetic code, up to three genes may be encoded simultaneously. The constraints placed on a nucleotide involved in such a multiple coding region will naturally have an effect on its mutational pattern, and as a result the concept of selection is complicated further. Another complication is the uncertainty of alignments when dealing with genomes of reasonable evolutionary distance. Recent papers have shown that parameter estimation can be greatly biased by the use of a fixed alignment [10] .