View Features in Multiple Sequence Alignments

How do I view sequence-associated features in a multiple sequence alignment?

SnapGene version 5.3 and later allow display of features in multiple sequence alignments.

SnapGene 6.0 and later allow editing of features in multiple alignments. See View or Edit Features in a Multiple Alignment.

Create a Multiple Alignment with Annotated Sequences

Prepare your annotated sequences for alignment, in this example the sequences are stored in a Collection.

Select the sequences for alignment, and click Align Selected Sequences....

Choose one or more Alignment algorithms to use and enter a name for the new alignment. Click Align to run the Aligner/s and create the new alignment/s.

View the Alignment

View the new alignment. By default features will not be displayed.

Click the disclosure triangle associated with a sequence to view the associated feature, including translation for CDS features.

Option-click (macOS) or ALT-click (Windows and Linux) on a disclosure triangle to expand and show the features for all sequences in the alignment.