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insertion/deletion:how to weigh in a DNA sequence matrix?

Arlin Stoltzfus arlin at is.dal.ca
Thu Nov 13 17:36:19 EST 1997

Arlin Stoltzfus wrote:
> than nucleotide characters.  One should reduce the weight of indels
> to the extent that there is greater variation in mutation rates
> for different specific indels than in mutation rates for different
> specific nucleotide substitutions.  

I shouldn't have said it that way.  What is important is the 
variance in the rates of particular types of character transitions 
(in this case, different types of indels vs. different types of 
nucleotide transitions).  If all the character transitions are 
neutral then (by the simple math of the neutral theory) the 
rates of change are numerically equal to mutation 
rates, which is why I was talking about variance in mutation 
rates.  Instead, I should be talking about rates of character 
change, but the basic argument would be the same, I expect.

Arlin Stoltzfus, Ph.D. (arlin at is.dal.ca)
Department of Biochemistry, Dalhousie University
Halifax, Nova Scotia B3H 4H7 CANADA
phone: 902-494-2968     fax: 902-494-1355

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