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): -
-Orders the sequences by the alphanumeric (0-9A-Za-z) -precedence of their names.
-Places sequences in the same group adjacent to eachother.
-Places pairs of sequences together that align with the greatest -fraction of conserved residues. -
-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->'.
- -
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
-alignment web services, the alignment ordering can be recovered by
-its corresponding entry in the 'Sort->By ..' menu.
-
+ 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. +
+
+ Sorting according to sequence features
+ Additional sort operations for alignments containing sequence
+ features are provided in the Feature
+ Settings dialog, opened via View→Feature
+ Settings...
+
+ 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 both cases, for sequences which are equivalent under the + sort operation, their order will be preserved (since version 2.10). + 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.