Sequences can be moved up and
down in the alignment:
Move sequences up and down
drag the name of the sequence up or down
When you move the mouse pointer over the label, the pointer will turn into a vertical arrow indicating that the sequence can be moved.
The sequences can also be sorted automatically to let you save time moving the sequences around. To sort the sequences alphabetically:
Right-click the name of a sequence | Sort Sequences Alphabetically
If you change the Sequence name (in the Sequence Layout view preferences), you will have to ask the program to sort the sequences again.
The sequences can also be sorted by similarity, grouping similar sequences together:
Right-click the name of a sequence | Sort Sequences by Similarity