Hello. I am not quite sure if these are the best newsgroups to ask this
in, but they seemed closest to the crux of my questions. I am currently
researching the evolutionary phylogeny of several sets of psuedogenes,
and one of the (obvious) tasks is to determine the evolutionary distance
between all of them.
I'm currently using GCG 8.1, and the Distances program does a very nice
job of calculating distances by several methods. My question concerns the
methods it uses, none of which I am familiar with. They include the
following:
*Kimura's two parameter method
*Tajima-Nei's method
*Jin-Nei's gamma distance method
*Jukes-Cantor method
I've found the 1990 paper by Tajima and Nei, but it doesn't shed much
light on what techniques are most appropriate/valid for a certain type of
sequence. If someone could point me to a site, or journal discussing the
pros and cons of each (or some of them), or pass along any pointers, I'd
*really* appreciate it.
John Blankenship
Department of Molecular Biotechnology
University of Washington
