Edit gaps in a sequence

With the release of MegAlign Pro 17.6 in 2024, you can insert, delete, or shuffle gaps in a sequence that is part of any multiple sequence alignment except a Mauve alignment.

To edit gaps:

1. Perform a multiple sequence alignment.

2. Click View > Style > Multiple Alignment. From the Layout drop-down menu, select Linear.
   
   

3. Open the Sequences view (View > Sequences > Show).

4. Edit one sequence row at a time using the instructions below.
   
   
   • To insert a gap, insert your cursor where you would like the gap to appear, then press the space bar or hyphen key ( – ). To insert a specific number of gaps, select the base where you would like to begin inserting gaps. Then type the number (e.g., 3) before using the space bar or hyphen key.
     
     
   • To delete a gap, select the gap you wish to remove, then press the backspace (←) or Delete key. To delete a specific number of gaps, select the first (leftmost) gap in the section you wish to delete. Then type the number (e.g., 3) and then use the backspace or Delete key.
     
     
   • To shuffle residues to the left or right of gaps, make a selection that includes both bases and gaps (“1” in the image below). Then, either press the left or right square bracket key ([ or ]), or use the Shuffle residues buttons ( ) in the view toolbar (2).
     
     
     
     The residues will all move in the direction indicated, and the gaps will move in the opposite direction (3).