Measures of non-synonymous substitutions

James McInerney james.o.mcinerney at
Mon Dec 15 12:28:26 EST 2003

Hi folks,

Could anybody tell me if there is a substantial difference between
estimating the rate of change in second positions of codons as a measure of
non-synonymous substitution rate versus using some of the other methods of
estimating this rate?

All changes in second positions are non-synonymous, therefore it should be a
reasonable estimate of the rate of fixation of non-synonymous substitutions
(although there are other positions where non-synonymous substitutions occur




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