Key Strokes

Jalview has two distinct modes of keyboard operation - in 'Normal' mode, single keystrokes (including those shown next to menu items) provide short cuts to common commands. In 'Cursor' mode (enabled by F2), some of these are disabled and more complex 'Compound Keystrokes' can be entered to perform precise navigation, selection and editing operations.

Key Which Mode Action
Escape Normal Clears the current selection region, highlighted columns and highlghted residues.
Escape Cursor As in normal mode, but also cancels any partially entered commands
F1 Both Show Help Documentation
F2 Toggle Cursor mode on / off
Control 'Z' Both Undoes the last sequence edit
Control 'Y' Both Redo the last sequence edit undone.
Up Arrow Normal Moves selected sequence(s) up the alignment
Down Arrow Normal Moves selected sequence(s) down the alignment.
Left Arrow Normal Slides selected sequence(s) left. Press Alt key to slide in cursor mode
Right Arrow Normal Slides selected sequence(s) right. Press Alt key to slide in cursor mode
Cursor Keys
(Arrow Keys) 		Cursor Move cursor around alignment
Page Up Both Scroll up the alignment view
Page Down Both Scroll down the alignment view
Control 'A' Both Selects all sequences in the alignment
Control 'I' Both Invert sequence selection.
Control Alt 'I' Both Invert column selection.
Control 'C' Both Copies the selected region into the clipboard as a Fasta format file
nb. not available in applet, as no clipboard is available
Control 'V' Both Paste the contents of the clipboard to the current alignment window. (Alignment Window->Edit->Paste->Add to this Alignment)
nb. if the paste is from a Jalview alignment, any sequence and alignment annotations will also be copied over.
Control Shift 'V' Both Paste the contents of the clipboard to a new alignment window. (Alignment Window->Edit->Paste->To New Alignment)
Control 'X' Both Cuts the (fully) selected sequences from the alignment.
Control 'F' Both Launches the search window
B Both Add highlighted columns to current column selection
Alt 'B' Both Add all but the currently highlighted columns to current selection
Control 'B' Both Toggle the column selection marks for the currently highlighted columns (or all others if Alt is also pressed)
H Both Hides / Reveals selected columns and sequences
Control 'H' Both Hides / Reveals selected columns
Shift 'H' Both Hides / Reveals selected sequences
Control + Shift 'H' Both Hides everything but the current selection
Control 'O' Both Input new alignment from file
Control 'S' Both Save alignment with current filename and format
Control Shift 'S' Both Save alignment as a new file or with a different format
Control 'P' Both Opens the print dialog box to print the current view
Control 'W' Both Closes the current view or the current alignment
Backspace Normal Delete the currently selected rows or columns from the alignment.
Control 'L' Left Remove columns to left of left-most column marker.
Control 'R' Both Remove columns to right of right-most column marker.
Control 'E' Both Remove gapped columns
Control Shift 'E' Both Remove all gaps
Control 'D' Both Open the 'Remove redundancy' Dialog box.
Normal

The compound commands available in the Cursor mode are summarised below. Single letter commands can be prefixed by digits to specify a repetition number, and some more complex commands take one or more numeric parameters (prefixing the command key and separated by commas).

Compound Command Mode Action (and parameter description)
0-9 Cursor Begin entering a numeric parameter (p) or repetition number for a cursor movement or edit command.
, Cursor Separates one or more numeric parameters (e.g. p1,p2) for a command.
p1,p2
Return		 Cursor Move cursor to a particular column (p1) and row (p2) in the alignment.
e.g. '5,6<Return>' moves the cursor to the 5th column in the 6th sequence.
pS Cursor Jump to the p'th sequence in the alignment.
pP Cursor Jump to p'th amino acid in current sequence.
pC Cursor Jump to p'th column in the alignment.
Q Cursor Marks the top left corner of the selection area
M Cursor Marks the bottom right corner of the selection area
[p]
Space		 Cursor Inserts one (or optionally p) gaps at the current position.
Hold down Control or Shift to insert gaps over a sequence group
[p]
Delete
 Cursor Removes one (or optionally p) gaps at the cursor position.
Hold down Control or Shift to insert gaps over a sequence group
[p]
Backspace
 Cursor Removes one (or optionally p) gaps at the cursor position.
Hold down Control or Shift to insert gaps over a sequence group