In some cases, you may have already aligned sequences, then decide to completely realign the same sequences plus certain selected unaligned sequences.
- Add sequences to the project and align some or all of them. If all sequences were aligned, add more sequences to the project.
- 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.
- (optional) An upcoming step will over-write the current alignment. Therefore, you may wish to save the original alignment before proceeding further.
- Specify which unaligned sequences to include in the new alignment by clicking on them or by using Ctrl/Cmd+click or Shift+click.
- Select Align > Realign with Selected Unaligned.
- Choose the desired alignment method from the drop-down menu, then set other options as desired.
- Press Align.
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