James says: "We have seen this case and we just handle it by saying that
selection has been very strong - just non-synonymous changes and no time for
observations of silent changes."
Actually, the system may be telling you something more Michael. There
is a powerful "genome phenotype" which acts on so-called silent sites. One
explanation of zero synonymous changes is, as James says, not time for
mutations to occur (e.g. a recent population bottle-neck). Another
explanation is that there has been selection against silent changes. For
more, in the context of the genome of a malaria parasite, please see:
Donald Forsdyke, Department of Biochemistry, Queen's University, Canada
"Michael Steiper" <steiper at fas.harvard.edu> wrote in message
news:aoi30d$niv$1 at mercury.hgmp.mrc.ac.uk...
>> 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
> Laboratory of Molecular Anthropology, Department of Anthropology
> Harvard University
>> lab#:617.495.8323 Peabody Museum
> office#:617.495.8323 11 Divinity Avenue
> www.fas.harvard.edu/~steiper/res.html Cambridge, MA 02138