Greetings,

I have added an analysis (due to Konrad Scheffler, Darren P. Martin, and Cathal Seoighe, University of Cape Town) which is capable for detecting whether or not there is evidence of positive selection (dN>dS) in an alignment which contains recombinant sequences. The paper describing the method can be found at Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login and the files implementing the analysis are in the 'Contributions' directory of the HyPhy distribution (builds of Aug 31st, 2006 or later).

Cheers,
Sergei