The File Menu is mainly used for creating new projects and opening and modifying existing ones. It has the following options available in it.
New Project (Ctrl+N)
Create and setup a new PopGen project. This opens the Project Setup Wizard.
Open Project (Ctrl+O)
Open an existing PopGen project file (*.pop).
Save Project (Ctrl+S)
Save the settings of the project.
Quit (Ctrl+Q)
Selecting this quits the whole application.