-<html>\r
-<head><title>Clustal Colour Scheme</title>\r
-<style type="text/css">\r
-<!--\r
-td {\r
- text-align: center;\r
-}\r
--->\r
-</style>\r
-</head>\r
-\r
-<body>\r
-<p><em>Clustal X Colour Scheme</em></p>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
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+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head><title>Clustal Colour Scheme</title>
+<style type="text/css">
+<!--
+td {
+ text-align: center;
+}
+-->
+</style>
+</head>
+
+<body>
+<p><strong>Clustal X Colour Scheme</strong></p>
<p>This is an emulation of the default colourscheme used for alignments in
- Clustal X, a graphical interface for the ClustalW multiple sequence alignment\r
+ Clustal X, a graphical interface for the ClustalW multiple sequence alignment
program. Each residue in the alignment is assigned a colour if the
amino acid profile of the alignment at that position
meets some minimum criteria specific for the residue type.</p>
<p>The table below gives these criteria as clauses: {+X%,xx,y},
- where X is the minimum percentage presence for any of the xx (or y) residue types.</p>\r
-<div align="center">\r
- <p> </p><table border="1">\r
+ where X is the minimum percentage presence for any of the xx (or y) residue types.</p>
+<div align="center">
+ <p> </p><table border="1">
<tr><th>Clustal X Default Colouring</th></tr>
- <tr> \r
- <td><table border="1">\r
+ <tr>
+ <td><table border="1">
<tr><th>Residue at position</th><th>Applied Colour</th><th>{ Threshhold, Residue group }</th></tr>
<tr><td>A,I,L,M,F,W,V</td><td bgcolor="#80a0f0">BLUE</td><td>{+60%, WLVIMAFCHP}</td></tr>
<tr><td>R,K</td><td bgcolor="#f01505">RED</td><td>{+60%,KR},{+80%, K,R,Q}</td></tr>
<tr><td>H,Y</td><td bgcolor="#15a4a4">CYAN</td><td>{+60%, WLVIMAFCHP}, {+85%, W,Y,A,C,P,Q,F,H,I,L,M,V}</td></tr>
<tr><td>P</td><td bgcolor="#c0c000">YELLOW</td><td>{+0%, P}</td></tr>
<tr><td>S,T</td><td bgcolor="#15c015">GREEN</td><td>{+60%, WLVIMAFCHP}, {+50%, TS}, {+85%,S,T}</td></tr>
-</table>\r
+</table>
</td></tr></table>
</div>
-</body>\r
-</html>\r
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff