To change the order of sequences in views:

Sequences may be rearranged one at a time or as contiguous groups using drag and drop. To move several sequences as a group, select them with Ctrl/Cmd+click or Shift+click, then drag them to the desired location and release the mouse button. Any ordering changes made to the Sequences view are simultaneously made to the Distance view and to the Overview.


To reorder sequences in the other views in the same order as the Tree view:

The Tree view sequences are ordered top-to-bottom in the vertical formats and left-to-right in the horizontal ones. This means that the order of sequence names shown in the phylogenetic tree may vary from ordering seen in the Sequences and Distance view and the Overview. To force the other views to reorder their sequences to agree with the Tree view, use Tree > Order Sequences Like Tree.

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