Shortcut keys for sequence navigation and editing

Below is a list of keyboard shortcuts you can use in the sequence editor to quickly move around, select and edit sequence.  Where keys differ between windows and mac, the windows key is listed first and the mac key is in italics (alt = option on mac).


1.  Navigating sequences and alignments

Left/Right arrow- Move by a single base

Up/Down arrow - Move by a single sequence

PgUp/PgDown - Move up or down by 10 sequences

Home/End - Move to beginning or end of sequence

Ctrl+[arrow key] | Alt+[arrow key] - Move 10 times further

Ctrl+[PgUp/PgDn] | Alt+[PgUp/PgDn] - Move to first/last sequence

Alt+[left mouse click] - Zoom in

Alt+shift+[left mouse click] - Zoom out

Alt+[mouse wheel] - Zoom

Alt+[click-drag] - Zoom on lassoed region

Ctrl+alt+[click-drag] | Command+alt+[click-drag] - Pan

Shift+ctrl+alt+[click-drag] | Shift+command+alt+[click-drag] - Fast Pan  

Shift+[mouse wheel] - Scroll horizontally


2.  Selecting sequences

Several options are available for selecting a region of sequence:

  • Mouse dragging: Click and hold down the left mouse button at the start position, and drag to the end position. Drag up or down to select multiple sequences across an alignment or sequence list.  To select multiple regions, select the first region then hold down ctrl or command and select the next regions.  
  • Select from annotations: When annotations are available, click on any annotation to select the annotated residues. As with mouse dragging, multiple selections can be made with the Ctrl or command key.
  • Click on sequence name: This will select the whole sequence.
  • Select all: Use the keyboard shortcut Ctrl+A (Command +A on Mac) to select everything in the panel.

Keyboard shortcuts for selecting sequences:

Double click - selects a single residue

Triple click - selects a block of residues within a single sequence

Quadruple click - selects a block of residues across multiple sequences

Shift+[click] - extends the selection to the specified position.  E.g. click at the beginning of the region you want to select, then hold down shift and click at the end position to select the bases in between.  

Ctrl+[click-drag] | Command+[click-drag] - Add to selection

Shift+[arrow key] - Extends selection by 1 base.   

Shift+ctrl+[arrow key] | Shift+alt+[arrow key] -  Extends selection by 10 bases at a time.  E.g to extend the selection across multiple sequences in the alignment, select the region you want in the first sequence, then shift+ [down arrow] or shift+alt+ [down arrow] to apply the selection to the sequences underneath.

Shift+ctrl+pgdn | Shift+alt+PgDn - Extends the selection in the first sequence to all sequences in the alignment (i.e. selects the entire column).  

Esc - Clear selection


3. Editing sequences:

Before a sequence or alignment can be edited, you must click the “Allow Editing” button.  Once edit mode is activated, you can insert or delete bases as you would in a regular text document.  Inserting and deleting bases adds or removes sequences to/from the right.  If you wish to add or remove sequences to or from the left, hold down the shift key while inserting or deleting.  

You can also use any of the standard editing operations such as Copy (ctrl/command+C), Cut (ctrl/command+X), and Paste (ctrl/command+V). To undo your changes at any time, press ctrl/command+Z. These operations are also under the main Edit menu.

Editing shortcut keys (requires editing mode to be activated):

Space or '-' - Insert Gap

Shift+Backspace/Delete - Moves residues from the left into the deleted area

Shift+[any residue] - Inserts a base and moves residues to the left

Click+Drag - Once you have selected a region of sequence, you can move it by clicking in the selection and dragging it with the mouse.  You can use this to quickly insert gaps in an alignment.

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