X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2Findex.html;h=b344330bc62fa80e342be6a89d0ac8ca500d4490;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=7aecc233c3bd7fdabe231306b7c68beb5bc5a48a;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/help/html/colourSchemes/index.html b/help/html/colourSchemes/index.html
index 7aecc23..b344330 100755
--- a/help/html/colourSchemes/index.html
+++ b/help/html/colourSchemes/index.html
@@ -1,20 +1,21 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * 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 
  * 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>Colour Schemes</title>
@@ -49,6 +50,7 @@ background, and the intensity threshold for transition between them.</p>
 <p>The default colour schemes are summarised in the table below:
 <div align="center">
 <p>&nbsp;</p>
+<p><strong>Protein Colour Schemes</strong></p>
 <table border="1">
 	<tr>
 		<td>
@@ -291,6 +293,81 @@ background, and the intensity threshold for transition between them.</p>
 		</td>
 	</tr>
 </table>
+<p>&nbsp;</p>
+<p><strong>Nucleotide Colour Schemes</strong></p>
+<table border="1">
+	<tr>
+		<td>
+		<table border="1">
+			<tr>
+				<td nowrap></td>
+				<td>A</td> <!--Adenine-->
+			    <td>C</td> <!--Cytosine-->
+    			<td>G</td> <!--Guanine-->
+    			<td>T</td> <!--Thymine-->
+    			<td>U</td> <!--Uracil-->
+    			<td>I</td> <!--Inosine-->
+    			<td>X</td> <!--Xanthine-->
+    			<td>R</td> <!--Unknown Purine-->
+    			<td>Y</td> <!--Unknown Pyrimidine-->
+    			<td>N</td> <!--Unknown-->
+    			<td>W</td> <!--Weak nucleotide (A or T)-->
+    			<td>S</td> <!--Strong nucleotide (G or C)-->
+    			<td>M</td> <!--Amino (A or C)-->
+    			<td>K</td> <!--Keto (G or T)-->
+    			<td>B</td> <!--Not A (G or C or T)-->
+    			<td>H</td> <!--Not G (A or C or T)-->
+    			<td>D</td> <!--Not C (A or G or T)-->
+    			<td>V</td> <!--Not T (A or G or C-->
+			</tr>
+			<tr>
+				<td height="24">Nucleotide</td>
+				<td bgcolor="#64F73F"></td>
+				<td bgcolor="#FFB340"></td>
+    			<td bgcolor="#EB413C"></td>
+    			<td bgcolor="#3C88EE"></td>
+    			<td bgcolor="#3C88EE"></td>
+    			<td></td>
+    			<td></td>
+    			<td></td>
+    			<td></td>
+    			<td></td>
+    			<td></td>
+    			<td></td>
+    			<td></td>
+    			<td></td>
+    			<td></td>
+    			<td></td>
+    			<td></td>
+    			<td></td>
+			</tr>
+			<tr>
+				<td height="24">Purine/Pyrimidine</td>
+				<td bgcolor="#FF83FA"></td>
+				<td bgcolor="#40E0D0"></td>
+    			<td bgcolor="#FF83FA"></td>
+    			<td bgcolor="#40E0D0"></td>
+    			<td bgcolor="#40E0D0"></td>
+    			<td></td>
+    			<td></td>
+    			<td bgcolor="#FF83FA"></td>
+    			<td bgcolor="#40E0D0"></td>
+    			<td></td>
+    			<td></td>
+    			<td></td>
+    			<td></td>
+    			<td></td>
+    			<td></td>
+    			<td></td>
+    			<td></td>
+    			<td></td>
+			</tr>
+		</table>
+		</td>
+	</tr>
+</table>
+
+
 </div>
 <p align="center">&nbsp;</p>
 </body>
