We apply our method to the HIV2 genomes J04542 with reasonably diverged 'descendants' U27200, M15390, DQ00835 and M30502, by splitting the genome into different regions whenever there is a change in gene structure. Setting all our initial parameters to 0.5, as above, we Simulation Results: Varying Evolutionary Distance Figure 1 Simulation Results: Varying Evolutionary Distance. Simulation results between two sequences for a double coding region of length 600 of varying evolutionary distance. The figure plots the average estimation error of the statistical method and the fixed alignment method using both ClustalW and GenAl, versus the evolutionary distance between the two sequences. The estimation error is measured as the fraction of the average absolute deviation to the true parameter value and the true value itself. The evolutionary distance is measured as a + 2b, where a and b are transition and transversion rates respectively. obtain a selection annotation for the different regions.