Almost any method will solve this problem correctly. The simplest way to calculate a distance between two sequences is to count the number of differences. This measure is often called the Hamming distance. It reflects the difference between sequences, but ignores their evolutionary relationship. This results in a difference of 1.
Many replication rounds later the same site gets mutated again.
If it becomes a T or a C, the differences doesn't change, but the evolutionary distance should increase, because there have now been two evolutionary events. The figure illustrates two things. First, the effect of the correction increases with the difference between the sequences, and is negligible with very homologous sequences. A relatively new development is the use of models that incorporate variable evolutionary rates across sites. Gary Olsen has a program called DNArates which can estimate the rates of evolution in different sites, given an initial tree.