Keyboard & mouse
Keyboard
| Shortcut | Action |
|---|---|
| Ctrl/⌘ + O | Open sequences or an alignment |
| Ctrl/⌘ + S | Save the current alignment |
| Ctrl/⌘ + C | Copy the selection (or whole alignment) as FASTA |
| Ctrl/⌘ + P | Pin the selected columns as trusted |
| Ctrl/⌘ + Shift + P | Unpin the selected columns |
| Ctrl/⌘ + Z | Undo the last edit |
| Ctrl/⌘ + Shift + Z | Redo |
| Ctrl/⌘ + T | Show the true alignment, read-only (needs a reference); again to go back |
Ctrl/⌘ + + |
Bigger text (zoom in) |
Ctrl/⌘ + - |
Smaller text (zoom out) |
Ctrl/⌘ + 0 |
Reset text size |
| Esc | Clear the column and sequence selection |
The residue font scales with the cells, so zooming makes the letters bigger or smaller. You can also use View ▾ → Bigger / Smaller / Reset text size, or Ctrl/⌘ + scroll over the alignment.
Editing with the keyboard
Editing acts on the selected sequences only. Click a cell to place the edit cursor (a bold amber box) and select that one sequence; Cmd/Ctrl-click more cells (or sequence names) to add them to the selection. Selected sequences are tinted amber. Then slide them with the keyboard. Sliding works at every view level: one base at the nucleotide level, or a whole codon (keeping the reading frame) at the codon / amino-acid level. Every edit is undoable.
| Gesture / Key | Action |
|---|---|
| Click a cell or name | Place the cursor and select that one sequence |
| Cmd/Ctrl-click a cell or name | Add / remove a sequence from the selection |
| Shift-click a cell or name | Select a contiguous range of sequences from the last click |
| Drag a selected (amber) sequence | Slide it (and any other selected sequences) left/right with the mouse — one column per column you drag |
| Alt/Option-drag any sequence | Grab and slide that sequence even if it wasn't selected |
| ← → ↑ ↓ | Move the edit cursor |
- (minus) or Space |
Slide the selected sequences one column right (opens a gap; absorbs a trailing gap rather than widening the whole alignment) |
| Backspace / Delete / Shift+Space | Slide the selected sequences one column left (consumes the gap to the left; refused if any selected sequence has no gap there) |
Hold - / Backspace (etc.) |
The key auto-repeats, so holding it slides continuously |
Tip
To realign one sequence against the rest, click it and either drag it into
place or tap / hold - and Backspace. To move several at once, Cmd-click each
one first (or Shift-click a range) — they slide together, keeping their
alignment relative to one another, while the unselected sequences stay put.
Sequence groups
If you keep moving the same set of sequences together (say, all the animals),
save them as a named group: select them, then Edit ▸ Sequence groups ▸ Save
selection as group…. Later, Edit ▸ Sequence groups ▸ Select “name” re-selects
all its members in one click, ready to slide together. Groups are stored in a small
companion file next to the alignment (<file>.craic.json) — the alignment file
itself stays a standard FASTA / Stockholm / etc. — and are restored when you reopen
the alignment.
Mouse
| Gesture | Action |
|---|---|
| Scroll | Pan the alignment vertically |
| Ctrl/⌘ + scroll | Zoom the cells and text in and out |
| Click-drag across columns | Select a column range (drives the sandbox and posterior explorer) |
| Single-click a residue | Probe it (paint the columns it could also align to) and place the edit cursor there |
| Drag a dock title bar | Move or float the Ambiguity tools panel |
Tip
A single click and a click-drag do different things: a click probes one residue without changing your column selection; a drag sets the selection that both ambiguity panels use.