+ 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.
+ + +