Key Strokes

Jalview responds a number of key strokes, and has two distinct modes of keyboard operation. The F2 key switches between 'Normal' and 'Cursor' mode operation.

As in normal mode, but also cancels any partially entered commandsShow Help DocumentationMoves selected sequence(s) up the alignmentMoves selected sequence(s) down the alignment.Cursor Keys
(Arrow Keys)
Pastes the contents of the clipboard to a new alignment window. (same as the Alignment Window menu Edit->Paste command)
nb. if the paste is from a Jalview alignment, any sequence and alignment annotations will also be copied over.
KeyWhich ModeAction
EscapeNormal Clears the current selection region, highlighted columns and highlghted residues.
EscapeCursor
F1Both
F2Toggle Cursor mode on / off
Control 'Z'BothUndoes the last sequence edit
Up ArrowNormal
Down ArrowNormal
CursorMove cursor around alignment
Control 'A'BothSelects all sequences in the alignment
Control 'C'BothCopies the selected region into the clipboard as a Fasta format file
nb. not available in applet, as no clipboard is available
Control 'V'Both
Control 'X'BothCuts the (fully) selected sequences from the alignment.
Control 'F'BothLaunches the search window
0-9CursorBegin entering a numeric parameter [p] for a cursor movement or edit command
,CursorSeparates one or more numeric parameters ([p1],[p2]) for a command.
[p1],[p2]ReturnCursorMove 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.
[p1]SCursorJump to the p1'th sequence in the alignment.
[p1]PCursorJump to p1'th amino acid in current sequence.
[p1]CCursorJump to p1'th column in the alignment.
QCursorMarks the top left corner of the selection area
MCursorMarks the bottom right corner of the selection area
[p1]SpaceCursorInserts p1 gaps at the current position.
p1 is optional. Hold down Control or Shift to insert gaps over a sequence group
[p1]DeleteCursorRemove p1 gaps at the cursor position.
p1 is optional. Hold down Control or Shift to insert gaps over a sequence group