• When I try to download and run ApE on my Mac, a dialog box pops up and says the application is damaged and should be put into the trash. How do I fix this?

Gatekeeper will report that the application is damaged and will prevent ApE from running.
You have to go to System Preferences > Security and Privacy > General.
Check "Allow software downloaded from anywhere" to allow ApE to run.
Apparently, right click on ApE and select "Open" will not work to bypass Gatekeeper on all systems.
Or use a command line function to change the quarantine attributes.
I may need to put ApE on the Apple store and start charging for it to get around this in the future.

  • When I search for XbaI, ClaI, BclI, etc. sites that I KNOW are in my sequence, ApE can't find them. Is your search function just a POS?

No, it is not a POS. You have the Dam/Dcm checkbox on for the sequence you are searching. ApE will try to represent how real restriction enzymes will react with acual DNA. If the DNA is purified from a source that will modify it with Dam/Dcm methylation, you want to have the box checked. If you are purifying from a source that will not modify it, you want to uncheck the box.

  • How do I run ApE on Mavericks?

Download the Mavericks version of ApE (found on the main page of the website).