Sometimes it is useful to be able to swap sequence domains in a sequence and/or alignment. For example, you may have several antibody sequences where the Light chain is listed before the Heavy chain and another sequence where the Heavy chain appears before the Light. In this case, you want to swap the order in that last sequence so that it matches the other sequences and you can then perform an alignment.

To do this, first display the sequences in Chain View by right clicking over the Sequence Window and choosing View | Chain View. Then select at least one residue in each chain and right click again over the Sequence Window and choose Chain and Domain | Swap Domains as shown below:

When switch back to Wrapped View or Extended View you will see that the chains have been swapped.