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 |
| 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 |