Sorting Sequences

Any group of selected sequences may be reordered by pressing the up or down arrow keys. The whole alignment may also be reordered by the use of the functions in the Sort menu (Calculate->Sort):

• Sort by ID

  Orders the sequences by the alphanumeric (0-9A-Za-z) precedence of their names.

• Sort by Group

  Places sequences in the same group adjacent to eachother.

• Sort by Pairwise Identity

  Sequences are ordered by decreasing fraction of conserved residues with respect to the first sequence in the alignment.

• Sort by Tree Order

  The leaf ordering of a particular phylogenetic tree is used to order the sequences corresponding to those leaves in the alignment.
  If a tree has been calculated from or associated with the current alignment, its name will appear in the submenu Sort->By Tree Order.

• Sort by alignment ordering

  Multiple alignment methods often order the sequences in their alignments by some measure of sequence identity.
  If the current alignment has been generated by one of Jalview's alignment web services, the alignment ordering can be recovered by its corresponding entry in the Sort menu:

If a sort is re-applied (by selecting the same menu item once again), the sequences will be sorted in the inverse order for that property. In the case of trees and alignment orderings, Jalview will remember your last choice for sorting the alignment and only apply the inverse ordering if you select the same tree or alignment ordering item again.