-<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</em></p>\r
- <p>Clustal X is a graphical interface for the ClustalW multiple sequence alignment\r
- program. Sequences can be coloured either by assigning a colour to specific\r
- residues, or on the basis of an alignment consensus. The residues in each\r
- column are coloured according to the consensus character assigned to that column.\r
- In this way, you can choose to highlight, for example, conserved hydrophilic\r
- or hydrophobic positions in the alignment. </p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * 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 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>
git://source.jalview.org / jalview.git / blobdiff