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.
|Multiple sequences||Use Ctrl/Cmd+click or Shift+click to select multiple sequences.|
|One entire sequence|| Either:
|A portion of all aligned sequences|| Drag the mouse across residues in the consensus sequence while holding down the left mouse button. 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.
|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), do any of the following:
|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:
|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.|
|One or more items in the Tree view||In the Tree view, to select one sequence, click on it. To select multiple sequences, use Ctrl/Cmd+click. To select all sequences in a clade, click the horizontal “stem” for that branch.|
|All variants in the Variants view||Choose Variants > Select > Select All. Remove the selection using Variants > Select > Select None.|
|Individual variants in the Variants view||Drag the mouse or by use Shift+click or Cmd/Ctrl+click. To select all rows except for the currently-selected rows, choose Variants > Select > Invert Selection.|
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