[GCG] Calculating Evolutionary Distances, How to..

John Blankenship dmt at u.washington.edu
Mon Jan 29 16:58:08 EST 1996

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 

*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 

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