The following procedure causes the selected sequences to be completely removed from the project, not simply moved to the “Unaligned Sequences” area.

To remove sequences from the project:

  1. Select one or more of the aligned or unaligned sequences in the Overview or Sequences View by clicking, Ctrl/Cmd+clicking or Shift*+clicking on the sequence name(s).
  1. To remove sequences, either:
    • Right-click on the list of sequence names, and select Remove Sequence(s) from the menu.

    • Press the Delete key or use Edit > Delete.
  1. Respond to the confirmation message that appears, if any. Different versions of the message appear, depending whether you have selected aligned and/or unaligned sequences. One example is shown below.


  • During multiple alignment, “guide trees” are created that govern the order in which sequences are aligned to each other, starting with the most similar pair. Guide trees, in turn, are based upon all possible pairwise relationships among the member sequences.
  • When one or more sequences are removed from an alignment, any column containing 100% gaps is removed from all of the remaining aligned sequences. No new guide tree (representing the remaining sequences) is calculated. Therefore, the resulting alignment may not be as good as one produced by performing a completely new alignment with the remaining sequences.
  • When features have been mapped to the consensus, removing sequences from the alignment or unaligning (using Align > Unalign All) will cause all features to be removed from the consensus sequence. This is because feature mapping may no longer be accurate, since the consensus sequence may have different gapping.

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