To edit sequence(s) or an alignment click the Allow Editing toolbar button.
You can manually enter or delete sequence, or use any of the standard editing operations, such as Copy (Ctrl/command+C), Cut (Ctrl/command+X), Paste (Ctrl/command+V), Paste Without Annotations (Shift+Ctrl/command+V), Paste Reverse Complement and Undo (Ctrl/command+Z). All operations are under the main Edit menu, or can be accessed by right-clicking in the sequence view and selecting the option from the popup window.
To insert sequence, click at the position where you want to insert the sequence and type or paste it in. Normally existing residues will be shifted to the right when you insert sequence; to get them to shift to the left hold down the Shift key as you insert the sequence. To overwrite sequence, select the sequence you wish to overwrite and type or paste the new sequence in.
To select sequences or regions of sequence, there are several options:
Sequences can be reordered within an alignment by clicking the sequence name and dragging.
Sequences can be removed from an alignment by right-clicking (Ctrl+click on Mac OS X) on the sequence name and choosing the remove sequence option. Alternatively, select the entire sequence (by clicking on the sequence name) and press the delete key.
To delete a region of a sequence or alignment, select the region and press the delete or backspace key. Normally this will move residues on the right into the deleted area. To move the residues on the left into the deleted area, hold down the Shift key while deleting.
To drag a sequence to the left or right, select the region you want to move, then click it again and drag it to the position you want. Dragging will either move residues over existing gaps or open new gaps when necessary. Dragging a selection consisting entirely of gaps moves the gaps to the new location.
After editing is complete, click Save to permanently save the new contents.