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Ka/Ks ratio

James McInerney james.o.mcinerney at may.ie
Wed Oct 16 09:35:25 EST 2002

On 15/10/02 4:59 am, "Michael Steiper" <steiper at fas.harvard.edu> wrote:

> Hi-
> 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.

Hi Michael,

When you have no synonymous changes on a branch and you have replacement
substitutions, then the PAML software might give you a Ka/Ks ratio of
999.99, which is just an upper limit imposed by Ziheng Yang (I believe).
This just means that it is thought that positive selection has been very
strong on this branch.

We have seen this case and we just handle it by saying that positive
selection has been very strong - just non-synonymous changes and no time for
observations of silent changes.


> 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.
> THanks,
> Michael Steiper

Dr. James O. McInerney,
Bioinformatics and Pharmacogenomics Laboratory,
Department of Biology, National University of Ireland,
Maynooth, Co. Kildare, Ireland.
P: +353 1 708 3860
F: +353 1 708 3845
E:james.o.mcinerney at may.ie


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