We annotate using our statistical alignment method described above, as well as performing parameter optimization on a fixed alignment produced by both GenAl [6] and ClustalW [20] . As we can see from Figure 1 , ClustalW gives consistently rather bad results, since it is not designed to deal with overlapping coding regions. Our method achieves better results than GenAl on sequences of evolutionary distance less than 0.8, but cannot quite compete with GenAl on sequences further apart. Here our estimation error is shown as the fraction between the average absolute deviation of our estimated parameters to the true parameter value and the true value itself.