The main window for gap4 contains File, Edit, View, Options, Experiments, Lists and Assembly menus.
The File menu includes database opening and copying functions and consensus calculation options.
The Edit menu contains options that alter the contents of the database.
The View menu contains options to look at the data at several levels of detail, and analytic functions which present their results graphically.
The Options menu contains options for configuring gap4.
The Experiments menu contains options to analyse the contigs and to suggest experimental solutions to problems.
The Lists menu contains a set of options for creating and editing lists for use in various parts of the program.
The Assembly menu contains various assembly and data entry methods.