The same thing applies for sequences. The former substitution is a transition and can happen readily while the latter is a transversion and occurs far less frequently. Hence it would be desirable to weight or to treat these substitutions in a different fashion. There is no reason why we should have used 1 for a residue match and 0 for a mismatch in the section on alignments. But more generally than this problem of simple weighting, there are also subtler problems.
Lets assume for the moment that all mutations occur with equal frequency.
Then you might think that the difference between two sequences could be calculated simply by counting the number of nucleotide differences between the species. Lets consider how this difference, this measure of distance changes over time. Figure 1 shows the difference expected between two sequences that have diverged at increasing times into the past. The proportion of differences are calculated simply by counting the number of nucleotide differences divided by the total length of the sequence. Here is rate of substitutions for the sequences and t is the length of time since the last common ancestor of these sequences.