If two sequences are 100% identical (or, at least at synonymous sites),
then there's nothing you can say about the rate of synonymous
substitution, it's an unknown. It's like dividing by zero, no matter how
you might think that you understand it to be "Infinity", it's just
undefined, full stop.
One method is to prune your tree of one of the "duplicate" sequences. How
many nonsynonymous sites are there? One or two? Many? I guess if there
are many, then you'd want to pursue this further in order to try to
convince yourself of positive selection, but if there's only a few then I
don't think you can say much and should just move on to other more
interesting comparisons ...
On 15 Oct 2002, Michael Steiper wrote:
>> I am trying to detect positive natural selection in a group of sequences
> using Ka/Ks comparisons. The problem is that my number of Ks is zero in
> one of my branches. With this zero in the denominator, I get undefined
> answers and strange results using the PAML program.
>> Has anyone seen a case like this? It seems like someone must have
> encountered this before, and I'd like to see how it was handled. Any
> other ideas might be helpful, too.
>> Michael Steiper
Aaron J Mackey
University of Virginia
amackey at virginia.edu