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): +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.
+precedence of their names.
Places sequences in the same group adjacent to eachother.
+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->'.
+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 the Jalview
+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->By ..' menu.
+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.