The first protein sequences were determined in the 1950s and the first DNA sequences in 1960s. The availability of two homologous (derived from common ancestor) sequences immediately posed the problems of how to count the true number of events in their common history, since only the totally effect of many events could be seen. Ie if an A had been turned into a C this could be done in many ways, for instance A to C or A to G to C using 1 or 2 events respectively. This lead to the need for probabilistic models that could evaluate the probability of different histories. This project explores some of the basic models.