As part of our study of 11 related genes in two gene clusters in two insect
species, we are trying to determine rates of nonsynonymous and synonymous
mutations per site (Dn, Ds) in coding DNA using MEGA. While the average base
conrtent of the coding DNA is around 54%, there is a marked avoidance of G at
synonymous positions. The number of transitions and transversions is not
otherwise unusual. Nevertheless, we have applied the Jukes-Cantor correction
option to the calculations in MEGA. We are aware of no special treatments for
sequences showing this phenomenon. Is what we are doing OK, or is there some
other (better) way to calculate nonsynonymous and synonymous substitution
rates (preferably with free or inexpensive software)?
Mail to: Ship To:
Dr. Gerald Bergtrom, Ph.D. Dr. Gerald Bergtrom, Ph.D.
Biological Sciences Dept. Biological Sciences Dept.
University of Wisconsin-Milwaukee University of Wisconsin-Milwaukee
P.O. Box 413 3209 North Maryland Avenue
Milwaukee, WI 53201 Milwaukee, WI 53211