You can sort sequences in alignment using the Sort submenu in the Actions main menu or from the context menu. Also, you can use the General Options Panel tab:

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It is possible to sort sequences in the selected rows region or the whole alignment. There are six ways to sort sequences:

• By name, ascending

• By name, descending

• By length, ascending

• By length, descending

• By leading gaps, ascending
• By leading gaps, descending