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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
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+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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+<head>
+<title>Clustal Colour Scheme</title>
+<style type="text/css">
+<!--
+td {
+ text-align: center;
+}
-->
</style>
</head>
<body>
-<p><em>Clustal X Colour Scheme</em></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
- 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>
-<div align="center">
- <p> </p><table border="1">
-<tr><th>Clustal X Default Colouring</th></tr>
- <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>N</td><td bgcolor="#15c015">GREEN</td><td>{+50%, N}, {+85%, N,Y}</td></tr>
-<tr><td>C</td><td bgcolor="#80a0f0">BLUE</td>
-<td>{+60%, WLVIMAFCHP}</td></tr>
-<tr><td>C</td><td bgcolor="#f08080">PINK</td>
-<td>{100%, C}</td></tr>
-<tr><td>Q</td><td bgcolor="#15c015">GREEN</td><td>{+60%,KR},{+50%,QE},{+85%,Q,E,K,R}</td></tr>
-<tr><td>E</td><td bgcolor="#c048c0">MAGENTA</td><td>{+60%,KR},{+50%,QE},{+85%,E,Q,D}</td></tr>
-<tr><td>D</td><td bgcolor="#c048c0">MAGENTA</td><td>{+60%,KR}, {+85%, K,R,Q}, {+50%,ED}</td></tr>
-<tr><td>G</td><td bgcolor="#f09048">ORANGE</td><td>{+0%, G}</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>
-</td></tr></table>
-</div>
+ <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 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>
+ <div align="center">
+ <p> </p>
+ <table border="1">
+ <tr>
+ <th>Clustal X Default Colouring</th>
+ </tr>
+ <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>N</td>
+ <td bgcolor="#15c015">GREEN</td>
+ <td>{+50%, N}, {+85%, N,Y}</td>
+ </tr>
+ <tr>
+ <td>C</td>
+ <td bgcolor="#80a0f0">BLUE</td>
+ <td>{+60%, WLVIMAFCHP}</td>
+ </tr>
+ <tr>
+ <td>C</td>
+ <td bgcolor="#f08080">PINK</td>
+ <td>{100%, C}</td>
+ </tr>
+ <tr>
+ <td>Q</td>
+ <td bgcolor="#15c015">GREEN</td>
+ <td>{+60%,KR},{+50%,QE},{+85%,Q,E,K,R}</td>
+ </tr>
+ <tr>
+ <td>E</td>
+ <td bgcolor="#c048c0">MAGENTA</td>
+ <td>{+60%,KR},{+50%,QE},{+85%,E,Q,D}</td>
+ </tr>
+ <tr>
+ <td>D</td>
+ <td bgcolor="#c048c0">MAGENTA</td>
+ <td>{+60%,KR}, {+85%, K,R,Q}, {+50%,ED}</td>
+ </tr>
+ <tr>
+ <td>G</td>
+ <td bgcolor="#f09048">ORANGE</td>
+ <td>{+0%, G}</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></td>
+ </tr>
+ </table>
+ </div>
</body>
</html>