We are given two sequences S 1 and S 2 , descended from a common ancestor, together with the gene structure G of S 1 -in the case of Figure 5 this is a genome with two genes which overlap. Say these genes code in GRFs 1 and 2 respectively. Let us first assume we already have an alignment between our two sequences, and we wish to understand the way selection works on different regions of the genome. An initial question to ask would be, whether single and double coding regions behave in the same way. We thus, as shown, partition the genome into five segments, making a split wherever a gene starts or stops. These five segments we then assign to be of one of three region-types: non-, single-and double coding. When considering the effect a mutation of the indicated nucleotide C in the overlapping region of S 1 might have, we must consider its coding role in both reading frames. In GRF1 it is in the third position of the codon AGC and in GRF2 in the second position of the codon GCT. In the genetic code the codon AGx codes for serine or argenine, depending on whether x is a purine or a pyrimidine, respectively. On the other hand GxT codes for four different amino acids, depending on the nature of x. Therefore a transition in the nucleotide C will have no effect on the amino acid encoded by GRF1, whereas a transversion will. In GRF2 on the other hand, both will result in a non-synonymous substitution. Additionally, the selection strengths acting on either gene might be different, due to one of them evolving faster than the other.