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[jalview.git] / help / html / webServices / clustalw.html
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+<html>\r
+<head><title>ClustalW Alignment</title></head>\r
+<body>\r
+<p><strong>ClustalW Alignments</strong></p>\r
+<p>ClustalW is a program for multiple sequence alignment. It works\r
+with both DNA and protein sequences, and can also perform profile\r
+profile alignments to align two or more multiple sequence\r
+alignments.</p>\r
+<p>\r
+Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) <br>\r
+CLUSTAL W: improving the sensitivity of progressive multiple\r
+sequence alignment through sequence weighting, position specific gap\r
+penalties and weight matrix choice.<br>\r
+<em>Nucleic Acids Research</em> <strong>22</strong> 4673-4680\r
+</p>\r
+<p>There are two versions of this alignment function, which will operate\r
+on the selected region, if any, or the whole sequence set:</p>\r
+<ul>\r
+<li><strong>Calculations&#8594;Web Service&#8594;Clustal\r
+Alignment..</strong><br>\r
+Aligns using the clustalW program, ignoring any gaps in the submitted\r
+sequence set.\r
+</li>\r
+<li><strong>Calculations&#8594;Web Service&#8594;Clustal\r
+Realign..</strong><br>\r
+Submits the sequences with existing gaps to clustalW, which will\r
+preserve existing gaps and re-align those regions which are not optimal.\r
+</li>\r
+</ul>\r
+</body>\r
+</html>\r