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 each other.
Sort by Pairwise Identity
Places pairs of sequences together that align with the greatest fraction of conserved residues.
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.
Sort by Score
This menu appears if the alignment contains any sequence associated alignment annotation with associated score values. Each entry is the label for a distinct group of sequence associated annotation scores which can be used for sorting.
Reversing the Order
Selecting any item from the Sort menu will sort sequences in an ascending order according to the property defining the sort. If the same sort is re-applied, the sequences will be sorted in the inverse order. 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.