X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Fmsaclient.html;h=d627c66e09d132d4bc5ff0a1951215e4ccad4e6c;hb=6f9d7b98943ecba292a9c0dd65b30c4d8150c98f;hp=0d413fc698ae66cbf1e36f4da346a6d96b9284d3;hpb=0696cffbccbb537be78d9fc2410589adbcd7be35;p=jalview.git
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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 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
-
-
-
-
+ 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
+ program. 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 2.2 - 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
+
+
+
+
+
+