Jalview's Menus

Menus are used in 3 places in Jalview - the "Desktop Menu", the "Alignment Menu" and the "Popup Menu".

The Desktop Menu is always visible and is the starting point for loading new alignments.

The Alignment Window Menus are accessible once an alignment has been opened.

The Popup Menus are opened by clicking with the right mouse button in the alignment display area or on a sequence label in the alignment window.
Mac Users: pressing CTRL whilst clicking the mouse/track pad is the same as a right-click. See your system's settings to configure your track-pad's corners to generate right-clicks.

The Annotations Menu is opened by right-clicking on an annotation row label or in an annotation row.