ApEA plasmid Editor (ApE) is a free, multi-platform application for visualizing, designing, and presenting biologically relevant DNA sequences. ApE provides a flexible framework for annotating a sequence manually or using a user-defined library of features. ApE can be used in designing plasmids and other constructs via in silico simulation of cloning methods such as PCR, Gibson assembly, restriction-ligation assembly and Golden Gate assembly.https://jorgensen.biology.utah.edu/wayned/ape/ape_plasmidbiotools:ape_plasmidDesktop applicationhttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/topic_0632Probes and primershttp://edamontology.org/topic_3125DNA binding siteshttp://edamontology.org/topic_3168SequencingMacWindowsLinuxOtherFree of chargehttp://edamontology.org/operation_0578Plasmid map drawinghttp://edamontology.org/operation_0308PCR primer designhttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_0310Sequence assemblyhttp://edamontology.org/operation_0365Restriction digesthttps://github.com/mwdavis2/ApERepository10.3389/fbinf.2022.81861936304290PMC9580900Erik M. Jorgensenjorgensen@biology.utah.eduPerson