I am trying learn how to use HYPHY to estimate if there is any positive selection acting on any of the sites. I decided to first use the example shown on page 27-30 of HyPhy: Hypothesis testing using phylogenies. I am using a windows version and using the p51.nex example. Here is where I got stuck.
I cannot seem to find the window shown in Figure 19 (is that only in the mac version?) and also cannot proceed to perform the posterior Bayes analysis becuase I cannot find the menu item CATEGORIES:DEFINE NEW VARIABLE  ?

This menu should be available in the window which opens after you invoke Categories Processor (not in the parameter display table window). I'll check by running HyPhy on a PC and get back to you.

HTH,
Sergei