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|
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