Multiple sequence alignment services can be accessed from either the Alignment or the JABAWS Alignment submenu of the Alignment Window's Web Service menu. When an entry from one of these menus is selected, either the currently selected residues, or the whole sequence set (if there is no selection or only one sequence is selected) will be submitted for multiple sequence alignment.

There are two kinds of multiple sequence alignment operations available:

• alignment - where a new alignment is constructed from the input
• realignment - where any aligned sequences will be used by the service to construct a profile based alignment of the remaining unaligned sequences.

Multiple Alignments of Sequences with hidden columns
Multiple alignment services are 'column separable' analysis operations. If the input contains hidden columns then each visible segment of the input sequence set will be submitted for alignment separately, and the results concatenated (with the hidden regions preserved) once all alignment functions have completed. Each sub-job's state is reported in its own tab:

Multiple Multiple Sequence Alignment sub jobs running at once