In some cases, you may have already aligned sequences, then decide to completely realign the same sequences plus certain selected unaligned sequences.

To align selected unaligned sequences with an existing alignment:

  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 over-write the current alignment. Therefore, you may wish to save the original alignment before proceeding further.
  1. Specify which unaligned sequences to include in the new alignment by clicking on them or by using Ctrl/Cmd+click or Shift+click.
  1. Select Align > Realign with Selected Unaligned.
  1. Choose the desired alignment method from the drop-down menu, then set other options as desired.
  1. Press Align.

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