Many new keyboard shortcuts have been added in Jalview 2.2 to make editing, selecting and navigating an alignment even easier. The selection commands in the Edit menu, and the alignment formatting controls within the View menu have also been moved into their own respective Select and Format menus.

Some of the more important new keystrokes are shown below :

• Page Up and Page Down scrolls through the alignment view.
• Control I inverts the currently selected sequence set, and Control Alt I will invert the currently selected set of columns.
• Control V will paste the contents of the clipboard to the current alignment window, and Control Shift V pastes the data to a new window.
• Control O opens the file browser for loading a new alignment or Jalview archive.
• Control S saves the alignment with the current filename and format, and Control Shift S opens the Save As... dialog box.
• Control T creates a new alignment view, and Control W closes the current view, or if none remain, then the whole alignment.
• Control E will remove gapped columns in the alignment.
• Control D opens the Remove Redundancy dialog box.