I have downloaded the HYPHY package for windows, it seems to me that the universal code is missing. I tried to test positive selection, I was  asked for the genetic code. When I chose the universal code  I get directed to choose a file in  the GeneticCodes folder. there is no universal cod file there. where is it?
thank you
Hanan    

Dear Hanan,

Seems like HyPhy is not finding the installation directory properly. Try to open the HyPhy installation directory with windows explorer, and launching HyPhy by double clicking the application icon there. If you made a shortcut to HyPhy and opened the program by double clicking the shortcut, it may not find the installation directory and, by extension, the genetic codes.

Universal genetic code is built into the code, by the way - all others (used by the interface anyway) are inside the GeneticCodes folder.

Cheers,
Sergei

Dear Sergei,
I had the same problem described by Hanan. I followed your instructions launch the HyPhy by clicking the application icon. Unfotunately, the problem persisted. How can I find the universal code?
Thanks in advance.

Iderval

Dear Iderval,

It turned out that WinZip may not preserve the directory structure of the .zip archive when it is expanded, if one of the options (to preserve said structure) is not checked.

Make sure that when you expand the .zip file with HyPhy, the resulting directory contains a number of folders in it, including things like 'TemplateBatchFiles' and 'GeneticCodes'. If all you see are a long list of files, then perhaps the appropriate WinZip option has not been set.

Hope this helps,
Sergei