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To add sequences to an opened alignment, click the Align sequence(s) to this alignment toolbar button:

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     <img src="/wiki/download/attachments/65929673/Adding Sequence to Alignment.png"/>
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Choose a file with the sequence(s) from the files system, and click Open.

Also, you can add an already opened sequence or sequences to the alignment. To do it, select the sequence object(s) in the Project View and click the Align sequence to this alignment toolbar button. The sequence(s) will be aligned to the alignment automatically.