Change the order of sequences

Whether preparing an image of a view for publication, or simply for ease of analysis, you may want to change the order of sequences in one or more views. For instance, you may wish to order the tree to create a pleasing image or to draw the viewer’s focus to a certain spot, or to allow for easier comparison.

The following methods allow you to reorder sequences in a view. Note that some commands require you to first select one or more sequences before using the command.

Task	Menu command	Views where shortcut is available via the Sort Sequences tool ()	Affects sequence order in…	Notes
Order selected sequences manually	In the Sequences view or Overview, drag and drop the sequence(s) in the desired position.	N/A	Overview and Sequences view
Order sequences automatically by name or length	Sequences > Order Sequences Ascending (or Descending) > By Name (or Length).	Overview, Sequences view and Distance view	Overview and Sequences view
Order sequences automatically by pairwise statistics	Distance > Order Sequences Ascending (or Descending) By Pairwise > Distance (or %Identity, %Similar, %Dissimilar, %Gaps, Identical, Similar, Dissimilar, Gap count, Gap length or Length).	Overview, Sequences view and Distance view	Overview, Sequences view and Distance view
Order sequences by distance from the top sequence in the Distance view table	Distance > Order Sequences by Distance from Top Sequence	Distance view	Overview, Sequences view and Distance view	If nothing is selected, you will instead see the command described in the next row.
Order sequences by distance from a selected sequence	Distance > Order Sequences by Distance from Selection	Distance view	Overview, Sequences view and Distance view	If anything is currently selected, you will instead see the the command described in the previous row.
Order sequences in the Tree view by depth or distance	Tree > Order Ascending (or Descending) By > Default Order (or Depth or Distance)	Tree view	Tree view	Default Order and Depth both sort in order of depth (i.e. by the sum of the branch lengths). Depth measures branching; the children of a subtree are sorted by the maximum number of branches to a leaf. Distance sorts in order of the distance between samples in the dataset. The children of a subtree are sorted by the maximum distance (i.e. length in one dimension) from the subtree node to a leaf. In this set of commands, Ascending and Descending are arbitrary terms referring to the display structure of the tree. Ascending tends to form a diagonal from the upper-left to lower right while Descending tends to form a diagonal from lower-left to upper-right.
Order sequences in all views to match the order in the Tree view	Tree > Order Sequences Like Tree	Tree view	Overview, Sequences view and Distance view