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):

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.