Reordering the Alignment

  1. For sequences in an alignment window, select a sequence in the sequence ID panel, and use the up and down arrow keys to alter the sequence’s position in the alignment. (Note that this will not work in cursor mode).

  2. Repeat but select a non-contiguous set of sequences by using the [CTRL] ([CMD] on Mac) key. Note how the sequences group together when they reach the top of the alignment.

For more information on this topic go to section 2.4 of the Jalview manual.
 This exercise can be viewed in the Reordering and hiding sequences in an alignments video.