We run our method on the Hepatitis B strand NC003977 and 'descendants' Woodchuck Hepatitis B strand J02442 and Ground Squirrel Hepatitis K02715, with sequences and gene structure downloaded from GenBank. As seed parameters we have all values set to 0.5 and wait between iterations for a difference in our loglikelihood of <1. Our method takes ~40 seconds to reach convergence and results are shown in Figure 3 .