To create an alignment, click on the "Alignment" icon on the right-side toolbar and choose "Create New Alignment".
After specifying the files to create an alignment against, navigate to the "Sequences" portion of the alignment pop-up window.
By default, the original sequence the alignment was created against is chosen as "Template". By clicking on the template sequence again, the template designation is removed, and a consensus alignment can be performed with all of the sequences included in this alignment. Alternatively, if you click on a different sequence, that new sequence will be designated as the template.