To merge unaligned sequences into the current project’s existing alignment:

In contrast to the “Profile alignment” method, this method retains existing gaps, and adds new gaps, if necessary.

  1. Add sequences to the project and align some or all of them. If all sequences were aligned, add more sequences to the project.
  1. Before proceeding, check that the “Unaligned Sequences” bars in the Overview and Sequences view display a number ≥ 1 in the parentheses. If you wish, you may show or hide the unaligned sequences by clicking the arrows on the left of each bar.

  1. (optional) An upcoming step will overwrite the current alignment. Therefore, you may wish to save the original alignment before proceeding further.
  1. Specify which unaligned sequences to add to the current alignment.
  1. Select Align > Merge Unaligned into Existing Alignment or press the Align sequences to an existing alignment tool (). The menu command and tool are enabled only if the project contains an alignment and at least one unaligned sequence.
  1. Choose the desired alignment method from the drop-down menu, then set other options as desired. The Mauve alignment method is not supported in this workflow.
  1. Press Align.

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