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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+
+Multiple Sequence Alignment Web Service
+
+
+ Multiple Sequence Alignment Web Services
+
+ Multiple sequence alignment services are accessed from the 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.
+
+ JABAWS Alignment services
+
Most alignment services are provided by the
+ JABAWS framework, which allows you to
+ customise the precise parameters used when running each alignment
+ prgoram. In addition to the 'Default settings', you may choose from a
+ range of alignment preset settings, or create your own using the
+ 'Edit Settings And Run ..' dialog
+ box.
+
+
+ Alignment programs supported by JABAWS.
Versions
+ shown are those bundled with JABAWS 2.01 - if you are using a
+ different server, check its home page to find out which versions are
+ provided.
+
+
+
+
+ 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
+
+
+
+ 
+
+
+
+