+++ /dev/null
-<html>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
- *
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- *
- * 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