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.
Cursor Keys (Arrow Keys) | Cursor | Move cursor around alignment. Press SHIFT to move cursor from an aligned region to next gap, or to the next aligned region when at a gap.
Cursor Keys (Arrow Keys) | Normal (+Alt in Cursor) | Moves selected sequence(s) up, down, left, or right according to the direction pressed. Alt+Arrow key to move selection or sequence under cursor in cursor mode.
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