ApE (A Plasmid Editor)

ApE provides a graphical environment for editing, visualizing, and analyzing DNA sequences. Users can view sequences as text maps that display translation, melting temperature, GC content, and open reading frames in real time, and can switch to linear or circular graphic maps where restriction sites are highlighted and features are linked via hyperlinks. The program supports reading common file formats such as DNA Strider, FASTA, GenBank, and EMBL, and can import ABI sequencing trace files, aligning them to reference sequences with clickable links back to the original trace.

The tool includes a virtual restriction digest that can generate user‑defined DNA ladders and display band positions, as well as functions for selecting sites based on frequency, type, or comparative cut patterns across multiple sequences. Built‑in and customizable feature libraries— including default and fluorescent protein collections—allow rapid annotation of plasmid components. Graphics can be exported as encapsulated PostScript or scalable vector files for publication or further editing.

ApE runs on macOS (OS X 10.11 and later, including Apple Silicon) and Windows (XP through 10). It offers both an inline feature view that shows annotations directly in the sequence window and a compact mode for large sequences, with preferences to toggle between them. The software is stable and maintained, with regular updates and documentation provided through a YouTube tutorial channel.