[Menu-bar> Help>Selected topics>Alignment panel] The keyboard is used to move the alignment cursor and to introduced/removed alignment gaps.
Cursor Movements
Ctrl+←To first residue
Ctrl+→To last residue
Alt+→ To next gap
Alt+← To previous gap
Home To first row
End To last row
Ctrl+Home To first residue
Ctrl+End to last residue

Movement of the view-port
PgDown Scroll down
PgUp Scroll up
Shift+PgUp Scroll left

Deleting gaps
Delete Delete gap right from or under cursor
Backspace Delete gap left from cursor
Ctrl+Delete Delete next gap right from the cursor
Ctrl+Backspace Delete next gap left from cursor
Ctrl+Shift+Delete Delete entire white space under cursor
Ctrl+Shift+BackspaceDelete entire white space left from cursor

Inserting gaps
Space Insert gap under cursor
Insert Insert gaps until next residue in above row is reached.
Ctrl+Ins Remove gaps until previous residue in above row is reached
Shift+InsInsert gaps until next residue in below row is reached

Repetition number. Performing an operation n times
4 2 Space Insert 42 gaps
4 2 DeleteDelete 42 gaps

Moving a sequence blocks: A group of consecutive residues that are not interrupted by gaps is moved left or right.
>Move right
<Move left

Ctrl+WClose alignment panel

Ctrl+KClose protein
Ctrl+*Display letters in better quality
U Upper Case
L Lower Case

Font Size
Ctrl++Zoom in
Ctrl+-Zoom out

Go to position
4 2 iMove cursor to residue index 42
4 r Move cursor to 4th row
4 2 cMove cursor to column 42
4 2 nMove cursor pdb-number 42

Save / restore position
SSave current cursor position
sRevert cursor position previously saved
4 SSave current cursor position to "4"
4 sRestore cursor position previously saved in "4"

The mouse actions follow general conventions:
  1. Sequence alignment
  2. Row-header
  3. Scroll-bar or alignment pane
Sequence groups
G xDefine all currently selected proteins as group "x".
g xLoad and select proteins of sequence group "x" if not already loaded. Select these proteins.
h xHide all proteins of sequence group "x".
u xUnselect all proteins of sequence group "x".

Sequence Groups:
Sequences can be grouped. Groups are designated by a digit or letter. The names of all proteins of a group are listed in a file in ./annotations/sequenceGroups/.