I started using HYPHY version 0.9920070529beta for MacOSX.  My colleague wrote me a batch file to conduct positive selection assays. This program called the file queryTree.bf in one of the HYPHY application folders. When I looked at my application folder in version 0.99 I could see a TemplateBatchFiles folder where the queryTree.bf was stored.

I recently upgraded to version 2.0. I now receive an error when I try to run HYPHY with my batch file since it cannot find the queryTree.bf file. When I look in my application folder I do not see the HYPHY subfolders as I did in version 0.99. What is the new location for the queryTree.bf file? How do I use my batch file in the newer version?
Thank you!