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SearchGUI is a user-friendly open-source graphical user interface for configuring and running proteomics identification search engines and de novo sequencing algorithms, currently supporting X! Tandem, MS-GF+, MS Amanda, MyriMatch, Comet, Tide, Andromeda, OMSSA, Novor and DirecTag. To start using SearchGUI, unzip the downloaded file, and double-click the SearchGUI-X.Y.Z.jar file. No additional installation required! The main purpose of SearchGUI is to make it simpler to use multiple search engines at the same time. We believe that a graphical user interface would be the best choice for most users, and therefore made SearchGUI with a graphical user interface. However, it can sometimes be easier to perform a search from the command line. For example when incorporating the search into some sort of pipeline. With this in mind we have therefore included the option of using SearchGUI as a command line tool.