Depending on the view, you can select one or more sequences, any portion of a sequence, or a specific portion of sequence corresponding to a feature. The active selection is highlighted in light blue. The selection can then be copied to the clipboard, copied in a specific format, exported to a file, exported to MegAlign, or realigned using different parameters and/or alignment method. This functionality is useful for sending a selected sequence or region of sequence to a new alignment project as an unaligned sequence. In this way, you can create a new document using a subset of the sequences in the current document, thereby avoiding having to find all of the input files. You can also use the selected region of one or more sequences to create a new document.

To select… Do this…
All sequences Click on the name of any sequence, then use Ctrl/Cmd+A or Edit > Select All.


  • In a Mauve alignment, this command extends the selection across the entire active block.

  • If a portion of sequence or alignment was originally selected, the entire sequence or alignment will be selected.

  • In the Distance view, this command selects the entire distance matrix.

  • If a subsequence was selected in one or all aligned sequences prior to using this command, this action will extend the subsequence selection to the full sequences.
Multiple sequences Use Ctrl/Cmd+click or Shift+click to select multiple sequences.
One entire sequence Either:

  • Click on the sequence name.

  • Drag the mouse across all residues in a sequence track while holding down the left mouse button.

  • Double-click on a feature that spans the entire sequence.
A portion of all aligned sequences Drag the mouse across residues in the consensus sequence while holding down the left mouse button.
A portion of one sequence Drag the mouse across residues in a sequence track while holding down the left mouse button.
The portion of a single sequence associated with a section of track (e.g. a Gap Fraction peak, etc.) Drag the mouse across the open track while holding down the left mouse button.
One or more tracks Click on a track to select it. To add additional tracks to the selection, use Ctrl/Cmd+click or Shift+click.
One or more features and corresponding sequence Click on a feature to select it. To add additional features to the selection, use Ctrl/Cmd+click.
The portion of a single sequence associated with a selected feature To expand a selection consisting of one or more features to a selection containing just the sequence corresponding to the feature(s), either:

  • Choose Edit > Select Subsequence or use the context (right-click) option of the same name.

  • Double-click on the feature under that sequence.
The portion of all aligned sequences associated with a feature To expand a selection consisting of one or more features or subsequence within a single sequence, to the corresponding subsequences across all aligned sequences or subsequences, either:

  • Choose Edit > Select Subsequences Across Alignment.

  • Triple-click on the feature under any of the sequences in the alignment.
Additional continuous items, when the first endpoint has been selected Use Ctrl/Cmd+Shift and click on the other endpoint.
The current selection, but expanded to encompass additional bases You can extend the length of an existing selection by Shift+clicking on the new endpoint. The selection will expand to use the chosen base as the new endpoint. If there are multiple selected ranges, the one closed to the chosen base will be expanded.


To toggle selection of items on or off, hold down the Ctrl/Cmd key while dragging the mouse, or while clicking on the items to toggle on or off.

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