Hi Sergei,
I am performing a local clock test exactly as appear in the manual "hyphy: hypothesis testing using phylogenies " p. 23. I am using your example data on HIV-1 Integrase. After fitting the model (MG94HKY85, the tree included with the data, local and partition) and saved the state as "Full Model" to be the alternative hypothesis. I select the branch (after double clicking tree in the parameter table). Then I invoke "show parameters in table" in the menu Tree. The two corresponding lines (node 9) appear as selected in the table. At this point I get a Windows with a Hyphy.exe error and the application is ended.

I am using pentium and windows XP.

Can you reproduce this error? any idea of what is happening? thank you very much in advance.

,
Antonio