Sequences can be removed from the alignment by right-clicking the label of a sequence:
right-click label | Delete Sequence
This can be undone by clicking Undo () in the Toolbar.
If you wish to delete several sequences, you can check all the sequences, right-click and choose Delete Marked Sequences. To show the checkboxes, you first have to click the Show Selection Boxes in the Side Panel.
A sequence can also be renamed:
right-click label | Rename Sequence
This will show a dialog, letting you rename the sequence. This will not affect the sequence that the alignment is based on.
Extra sequences can be added to the alignment by creating a new alignment where you select the current alignment and the extra sequences (see Create alignments).
The same procedure can be used for joining two alignments.