Copyright 1986-1993 by Joseph Felsenstein and by the University of Washington. Written by Joseph Felsenstein. Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed. This program implements the compatibility method for DNA sequence data.
Different lineages evolve independently.
The ancestral base at each site is unknown. The rates of change in most sites over the time spans involved in the the divergence of the group are very small. A few of the sites have very high rates of change. We do not know in advance which are the high and which the low rate sites. There is, however, some reason to believe that the present criterion is not the proper way to correct for the presence of some sites with high rates of change in nucleotide sequence data.