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+
+Multiple Sequence Alignment Web Service
+
+
+Multiple Sequence Alignment Web Services
+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.
+
+The JABAWS Alignment services also offer a
+range of predefined alignment settings and the opportunity for you to
+define your own set of parameters for running the alingment program.
+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
+
+
+
+
+
+