--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
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+ * of the License, or (at your option) any later version.
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+ -->
+<head>
+<title>Reference Sequences</title>
+</head>
+<body>
+ <p>
+ <strong>Reference Sequence Alignment Views</strong>
+ </p>
+ <p>
+ The reference sequence for an alignment is indicated by its ID being
+ shown in bold. When a reference sequence has been defined, the <strong>Format→Show
+ unconserved</strong> option highlights mutations with respect to the
+ reference sequence, rather than the alignment's consensus sequence.
+ </p>
+ <p>
+ <ul>
+ <li>Jalview automatically assigns a reference sequence when <a
+ href="../webServices/jnet.html"
+ >JPred4</a> predictions are imported.
+ </li>
+ <li><strong>Assigning a reference sequence</strong><br /> A
+ sequence can be marked as the reference sequence by right-clicking
+ on it's ID to open the popup menu, and selecting the "<strong>(Sequence
+ ID)→Mark as Reference</strong>" entry."</li>
+ </ul>
+ <p>
+ <em>Reference sequence based alignment visualisation was
+ introduced in Jalview 2.9.</em>
+ </p>
+</html>
git://source.jalview.org / jalview.git / blobdiff