ApE (A Plasmid Editor)

About

ApE (A Plasmid Editor), by M. Wayne Davis, is a plasmid editor for Mac (OS X 10.11 and later, with M1 Universal support). The current version is 3.1.10.1, and the developer provides a user manual, a list of updates and bug fixes, slide presentations describing features, a YouTube channel with tutorial videos, and downloadable demo theme files for circular graphic maps. The site also offers new Default Features and Fluorescent Proteins Features libraries, and new installs open in inline feature mode, which shows the bottom strand and features in the sequence window. This view can be turned off in Preferences (Settings) for large sequences or a compact layout.

ApE is also available for Linux, and some Windows systems may need Windows Defender temporarily disabled to install it. Older versions can be downloaded from the site. The site notes that if ApE misses restriction sites you expect to be present (such as ClaI, XbaI, or BclI), you can turn off Dam/Dcm methylation for the sequence and search again.