A novel method for estimating substitution rate variation among sites in alarge dataset of homologous DNA sequences

We present here a novel method to estimate the site-specific relative varia bility in large sets of homologous sequences. It is based on the simple ide a that the more closely related are the compared sequences, the higher the probability of observing nucleotide changes at rapidly evolving sites. A si mulation study has been carried out to support the reliability of the metho d, which has been applied also to analyzing the site variability of all ava ilable human sequences corresponding to the two hypervariable regions of th e mitochondrial D-loop.