I can't find alignments I've previously made. Where are they?

Alignments live on the sequence where they're aligned, under the alignment button on the right. At the moment, you cannot save alignments independently. 

My traces are not maintained on my alignments. 

In order to save traces (and not just the consensus sequence), import in your .ab1 trace data through the alignment button rather than through general import buttons.

How do I specify a template sequence?

When you are creating an alignment, click a sequence in the Sequences list to mark it as the Template sequence. Clicking the sequence again will remove the template designation, and switch to a consensus alignment.

How do I align multiple sequences at once?

After importing your sequences onto Benchling, expand the view (arrow on the top left), select multiple files, and then hit More --> Analyze --> Alignment. 

How do I trim traces that I'm aligning?

Using the bars on the left or right of the traces, drag these to trim the trace. The trimmed sections (greyed out) will be ignored in the alignment after you re-align.

Can I re-align after trimming? 

To re-align a trimmed trace, use the Realign button at the top of the alignment window. 

Can I rearrange the order of sequences in my alignment?

Yes. You can drag a sequence in your alignment by clicking on the left most region of the gray title area. Simply move it to the location you want in the alignment and let go.

How can I add new sequences to an existing alignment?

You can add additional sequences to an existing alignment by clicking the Realign button within the alignment tool.

How can I use a mouse to scroll the alignment horizontally?

You can scroll horizontally by pressing Shift while scrolling with the mouse wheel.

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