+<html>\r
+<head>\r
+<title>Multiple Sequence Alignment Web Service</title>\r
+</head>\r
+<body>\r
+<strong>Multiple Sequence Alignment Web Services</strong>\r
+<p>\r
+Multiple sequence alignment services are accessed from the <strong>Web\r
+Service→Alignment</strong> menu. When an entry from this menu is\r
+selected, either the currently selected residues, or the whole\r
+sequence set (if there is no selection or only one sequence is\r
+selected) will be submitted for multiple sequence alignment.\r
+</p>\r
+<p>There are two kinds of multiple sequence alignment operations\r
+available:<ul>\r
+<li><em>alignment</em> - where a new alignment is constructed from the input\r
+</li>\r
+<li><em>realignment</em> -\r
+where any existing alignments in the input are passed to the service\r
+for profile based alignment.\r
+</li>\r
+</ul>\r
+</p>\r
+<p>\r
+<strong>Multiple Alignments of Sequences with hidden columns</strong><br>\r
+Multiple alignment services are 'column separable' analysis\r
+operations. If the input contains <a\r
+href="../features/hiddenRegions.html">hidden columns</a> then each\r
+visible segment of the input sequence set will be submitted for\r
+alignment separately, and the results concatenated (with the hidden\r
+regions preserved) once all alignment functions have completed. Each\r
+sub-job's state is reported in its own tab:\r
+<p><center><strong>Multiple Multiple Sequence Alignment sub jobs running at\r
+once</strong><center></p>\r
+<center><img src="multimafftjbs.gif" align="centre"></center>\r
+</p>\r
+</body>\r
+</html>\r