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:
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: