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Ka/Ks ratio

Michael Steiper steiper at fas.harvard.edu
Mon Oct 14 22:59:31 EST 2002


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

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