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.