saturation of synonymous substitution

Bob Friedman friedmar at
Thu Apr 12 09:51:56 EST 2001

It means that enough synonymous substitutions have taken place between two
DNA sequences so that the pairwise sequence comparison approximately
resembles any two random sequences.  Most of the synonymous substitutions
happen at the 3rd position, so you can roughly say the 3rd positions are
saturated.  In an evolutionary context: the sequences have diverged
sufficiently so the 3rd positions are not useful for evolutionary
reconstruction, try using the nonsynonymous substitutions (or 1st and 2nd
positions).  Eventually dN also becomes saturated.
Bob Friedman

"Roland Hilgarth" wrote in message
> I have a question concerning synonymous substitution calculations.  When
> the rate odf synonymous substitutions per site (ds) the synonymous sites
> become saturated.  What exactly does synonymous site saturation mean in
> an evolutionary context?


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