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JAL-1027 JAL-1167 documentation and patched DNA/RNA matrix
authorjprocter <jprocter@compbio.dundee.ac.uk>
Thu, 6 Sep 2012 14:19:40 +0000 (15:19 +0100)
committerjprocter <jprocter@compbio.dundee.ac.uk>
Thu, 6 Sep 2012 14:19:40 +0000 (15:19 +0100)
help/html/calculations/scorematrices.html [new file with mode: 0644] patch | blob
src/jalview/schemes/ResidueProperties.java patch | blob | history

diff --git a/help/html/calculations/scorematrices.html b/help/html/calculations/scorematrices.html
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@@ -0,0 +1,95 @@
+<html>
+<head>
+<title>Substitution matrices in Jalview</title>
+</head>
+<body>
+<strong>Substitution Matrices available in Jalview</strong>
+<p>Jalview includes a small number of built in substitution matrices, used for different types of analysis.</p>
+<ul>
+<li><a href="#blosum62">BLOSUM62</a> is the standard protein sequence alignment and analysis matrix.</li>
+<li><a href="#pam250">PAM250</a> is another standard protein matrix, but not currently available for use from Jalview's user interface.</li>
+<li><a href="#simplenucleotide">Simple Nucleotide Substition</a> is a (fairly) arbitrary DNA/RNA substitution matrix.
+</li>
+</ul>
+
+<p><strong><a name="blosum62"></a>BLOSUM62</strong><br/>
+<table border="1">
+<tr><td></td><td>&nbsp;A&nbsp;</td><td>&nbsp;B&nbsp;</td><td>&nbsp;C&nbsp;</td><td>&nbsp;D&nbsp;</td><td>&nbsp;E&nbsp;</td><td>&nbsp;F&nbsp;</td><td>&nbsp;G&nbsp;</td><td>&nbsp;H&nbsp;</td><td>&nbsp;I&nbsp;</td><td>&nbsp;K&nbsp;</td><td>&nbsp;L&nbsp;</td><td>&nbsp;M&nbsp;</td><td>&nbsp;N&nbsp;</td><td>&nbsp;P&nbsp;</td><td>&nbsp;Q&nbsp;</td><td>&nbsp;R&nbsp;</td><td>&nbsp;S&nbsp;</td><td>&nbsp;T&nbsp;</td><td>&nbsp;U&nbsp;</td><td>&nbsp;V&nbsp;</td><td>&nbsp;W&nbsp;</td><td>&nbsp;X&nbsp;</td><td>&nbsp;Y&nbsp;</td><td>&nbsp;Z&nbsp;</td></tr>
+<tr><td>A</td><td>4</td><td>-2</td><td>0</td><td>-2</td><td>-1</td><td>-2</td><td>0</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td><td>1</td><td>0</td><td>0</td><td>0</td><td>-3</td><td>0</td><td>-2</td><td>-1</td></tr>
+<tr><td>B</td><td>-2</td><td>4</td><td>-3</td><td>4</td><td>1</td><td>-3</td><td>-1</td><td>0</td><td>-3</td><td>0</td><td>-4</td><td>-3</td><td>3</td><td>-2</td><td>0</td><td>-1</td><td>0</td><td>-1</td><td>-1</td><td>-3</td><td>-4</td><td>-1</td><td>-3</td><td>1</td></tr>
+<tr><td>C</td><td>0</td><td>-3</td><td>9</td><td>-3</td><td>-4</td><td>-2</td><td>-3</td><td>-3</td><td>-1</td><td>-3</td><td>-1</td><td>-1</td><td>-3</td><td>-3</td><td>-3</td><td>3</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>-2</td><td>-2</td><td>-2</td><td>-3</td></tr>
+<tr><td>D</td><td>-2</td><td>4</td><td>-3</td><td>6</td><td>2</td><td>-3</td><td>-1</td><td>-1</td><td>-3</td><td>-1</td><td>-4</td><td>-3</td><td>1</td><td>-1</td><td>0</td><td>-2</td><td>0</td><td>-1</td><td>-1</td><td>-3</td><td>-4</td><td>-1</td><td>-3</td><td>1</td></tr>
+<tr><td>E</td><td>-1</td><td>1</td><td>-4</td><td>2</td><td>5</td><td>-3</td><td>-2</td><td>0</td><td>-3</td><td>1</td><td>-3</td><td>-2</td><td>0</td><td>-1</td><td>2</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>-3</td><td>-1</td><td>-2</td><td>4</td></tr>
+<tr><td>F</td><td>-2</td><td>-3</td><td>-2</td><td>-3</td><td>-3</td><td>6</td><td>-3</td><td>-1</td><td>0</td><td>-3</td><td>0</td><td>0</td><td>-3</td><td>-4</td><td>-3</td><td>-3</td><td>-2</td><td>-2</td><td>-1</td><td>-1</td><td>1</td><td>-1</td><td>3</td><td>-3</td></tr>
+<tr><td>G</td><td>0</td><td>-1</td><td>-3</td><td>-1</td><td>-2</td><td>-3</td><td>6</td><td>-2</td><td>-4</td><td>-2</td><td>-4</td><td>-3</td><td>0</td><td>-2</td><td>-2</td><td>-2</td><td>0</td><td>-2</td><td>-1</td><td>-3</td><td>-2</td><td>-1</td><td>-3</td><td>-2</td></tr>
+<tr><td>H</td><td>-2</td><td>0</td><td>-3</td><td>-1</td><td>0</td><td>-1</td><td>-2</td><td>8</td><td>-3</td><td>-1</td><td>-3</td><td>-2</td><td>1</td><td>-2</td><td>0</td><td>0</td><td>-1</td><td>-2</td><td>-1</td><td>-3</td><td>-2</td><td>-1</td><td>2</td><td>0</td></tr>
+<tr><td>I</td><td>-1</td><td>-3</td><td>-1</td><td>-3</td><td>-3</td><td>0</td><td>-4</td><td>-3</td><td>4</td><td>-3</td><td>2</td><td>1</td><td>-3</td><td>-3</td><td>-3</td><td>-3</td><td>-2</td><td>-1</td><td>-1</td><td>3</td><td>-3</td><td>-1</td><td>-1</td><td>-3</td></tr>
+<tr><td>K</td><td>-1</td><td>0</td><td>-3</td><td>-1</td><td>1</td><td>-3</td><td>-2</td><td>-1</td><td>-3</td><td>5</td><td>-2</td><td>-1</td><td>0</td><td>-1</td><td>1</td><td>2</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>-3</td><td>-1</td><td>-2</td><td>1</td></tr>
+<tr><td>L</td><td>-1</td><td>-4</td><td>-1</td><td>-4</td><td>-3</td><td>0</td><td>-4</td><td>-3</td><td>2</td><td>-2</td><td>4</td><td>2</td><td>-3</td><td>-3</td><td>-2</td><td>-2</td><td>-2</td><td>-1</td><td>-1</td><td>1</td><td>-2</td><td>-1</td><td>-1</td><td>-3</td></tr>
+<tr><td>M</td><td>-1</td><td>-3</td><td>-1</td><td>-3</td><td>-2</td><td>0</td><td>-3</td><td>-2</td><td>1</td><td>-1</td><td>2</td><td>5</td><td>-2</td><td>-2</td><td>0</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td></tr>
+<tr><td>N</td><td>-2</td><td>3</td><td>-3</td><td>1</td><td>0</td><td>-3</td><td>0</td><td>1</td><td>-3</td><td>0</td><td>-3</td><td>-2</td><td>6</td><td>-2</td><td>0</td><td>0</td><td>1</td><td>0</td><td>-1</td><td>-3</td><td>-4</td><td>-1</td><td>-2</td><td>0</td></tr>
+<tr><td>P</td><td>-1</td><td>-2</td><td>-3</td><td>-1</td><td>-1</td><td>-4</td><td>-2</td><td>-2</td><td>-3</td><td>-1</td><td>-3</td><td>-2</td><td>-2</td><td>7</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-2</td><td>-2</td><td>-4</td><td>-2</td><td>-3</td><td>-1</td></tr>
+<tr><td>Q</td><td>-1</td><td>0</td><td>-3</td><td>0</td><td>2</td><td>-3</td><td>-2</td><td>0</td><td>-3</td><td>1</td><td>-2</td><td>0</td><td>0</td><td>-1</td><td>5</td><td>1</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>-2</td><td>-1</td><td>-1</td><td>3</td></tr>
+<tr><td>R</td><td>-1</td><td>-1</td><td>-3</td><td>-2</td><td>0</td><td>-3</td><td>-2</td><td>0</td><td>-3</td><td>2</td><td>-2</td><td>-1</td><td>0</td><td>-2</td><td>1</td><td>5</td><td>-1</td><td>-1</td><td>-1</td><td>-3</td><td>-3</td><td>-1</td><td>-2</td><td>0</td></tr>
+<tr><td>S</td><td>1</td><td>0</td><td>-1</td><td>0</td><td>0</td><td>-2</td><td>0</td><td>-1</td><td>-2</td><td>0</td><td>-2</td><td>-1</td><td>1</td><td>-1</td><td>0</td><td>-1</td><td>4</td><td>1</td><td>0</td><td>-2</td><td>-3</td><td>0</td><td>-2</td><td>0</td></tr>
+<tr><td>T</td><td>0</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-2</td><td>-2</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>0</td><td>-1</td><td>-1</td><td>-1</td><td>1</td><td>5</td><td>0</td><td>0</td><td>-2</td><td>0</td><td>-2</td><td>-1</td></tr>
+<tr><td>U</td><td>0</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td></tr>
+<tr><td>V</td><td>0</td><td>-3</td><td>-1</td><td>-3</td><td>-2</td><td>-1</td><td>-3</td><td>-3</td><td>3</td><td>-2</td><td>1</td><td>1</td><td>-3</td><td>-2</td><td>-2</td><td>-3</td><td>-2</td><td>0</td><td>-1</td><td>4</td><td>-3</td><td>-1</td><td>-1</td><td>-2</td></tr>
+<tr><td>W</td><td>-3</td><td>-4</td><td>-2</td><td>-4</td><td>-3</td><td>1</td><td>-2</td><td>-2</td><td>-3</td><td>-3</td><td>-2</td><td>-1</td><td>-4</td><td>-4</td><td>-2</td><td>-3</td><td>-3</td><td>-2</td><td>-2</td><td>-3</td><td>11</td><td>-2</td><td>2</td><td>-3</td></tr>
+<tr><td>X</td><td>0</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td></tr>
+<tr><td>Y</td><td>-2</td><td>-3</td><td>-2</td><td>-3</td><td>-2</td><td>3</td><td>-3</td><td>2</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-2</td><td>-3</td><td>-1</td><td>-2</td><td>-2</td><td>-2</td><td>-1</td><td>-1</td><td>2</td><td>-1</td><td>7</td><td>-2</td></tr>
+<tr><td>Z</td><td>-1</td><td>1</td><td>-3</td><td>1</td><td>4</td><td>-3</td><td>-2</td><td>0</td><td>-3</td><td>1</td><td>-3</td><td>-1</td><td>0</td><td>-1</td><td>3</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>-3</td><td>-1</td><td>-2</td><td>4</td></tr>
+</table>
+<p><strong><a name="pam250">PAM250</a></strong><br/>
+<table border="1">
+<tr><td></td><td>&nbsp;A&nbsp;</td><td>&nbsp;B&nbsp;</td><td>&nbsp;C&nbsp;</td><td>&nbsp;D&nbsp;</td><td>&nbsp;E&nbsp;</td><td>&nbsp;F&nbsp;</td><td>&nbsp;G&nbsp;</td><td>&nbsp;H&nbsp;</td><td>&nbsp;I&nbsp;</td><td>&nbsp;K&nbsp;</td><td>&nbsp;L&nbsp;</td><td>&nbsp;M&nbsp;</td><td>&nbsp;N&nbsp;</td><td>&nbsp;P&nbsp;</td><td>&nbsp;Q&nbsp;</td><td>&nbsp;R&nbsp;</td><td>&nbsp;S&nbsp;</td><td>&nbsp;T&nbsp;</td><td>&nbsp;U&nbsp;</td><td>&nbsp;V&nbsp;</td><td>&nbsp;W&nbsp;</td><td>&nbsp;X&nbsp;</td><td>&nbsp;Y&nbsp;</td><td>&nbsp;Z&nbsp;</td></tr>
+<tr><td>A</td><td>2</td><td>0</td><td>-2</td><td>0</td><td>0</td><td>-3</td><td>1</td><td>-1</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>0</td><td>1</td><td>0</td><td>-2</td><td>1</td><td>1</td><td>0</td><td>0</td><td>-6</td><td>0</td><td>-3</td><td>0</td></tr>
+<tr><td>B</td><td>0</td><td>3</td><td>-4</td><td>3</td><td>3</td><td>-4</td><td>0</td><td>1</td><td>-2</td><td>1</td><td>-3</td><td>-2</td><td>2</td><td>-1</td><td>1</td><td>-1</td><td>0</td><td>0</td><td>-1</td><td>-2</td><td>-5</td><td>-1</td><td>-3</td><td>2</td></tr>
+<tr><td>C</td><td>-2</td><td>-4</td><td>12</td><td>-5</td><td>-5</td><td>-4</td><td>-3</td><td>-3</td><td>-2</td><td>-5</td><td>-6</td><td>-5</td><td>-4</td><td>-3</td><td>-5</td><td>-4</td><td>0</td><td>-2</td><td>-3</td><td>-2</td><td>-8</td><td>-3</td><td>0</td><td>-5</td></tr>
+<tr><td>D</td><td>0</td><td>3</td><td>-5</td><td>4</td><td>3</td><td>-6</td><td>1</td><td>1</td><td>-2</td><td>0</td><td>-4</td><td>-3</td><td>2</td><td>-1</td><td>2</td><td>-1</td><td>0</td><td>0</td><td>-1</td><td>-2</td><td>-7</td><td>-1</td><td>-4</td><td>3</td></tr>
+<tr><td>E</td><td>0</td><td>3</td><td>-5</td><td>3</td><td>4</td><td>-5</td><td>0</td><td>1</td><td>-2</td><td>0</td><td>-3</td><td>-2</td><td>1</td><td>-1</td><td>2</td><td>-1</td><td>0</td><td>0</td><td>-1</td><td>-2</td><td>-7</td><td>-1</td><td>-4</td><td>3</td></tr>
+<tr><td>F</td><td>-3</td><td>-4</td><td>-4</td><td>-6</td><td>-5</td><td>9</td><td>-5</td><td>-2</td><td>1</td><td>-5</td><td>2</td><td>0</td><td>-3</td><td>-5</td><td>-5</td><td>-4</td><td>-3</td><td>-3</td><td>-2</td><td>-1</td><td>0</td><td>-2</td><td>7</td><td>-5</td></tr>
+<tr><td>G</td><td>1</td><td>0</td><td>-3</td><td>1</td><td>0</td><td>-5</td><td>5</td><td>-2</td><td>-3</td><td>-2</td><td>-4</td><td>-3</td><td>0</td><td>0</td><td>-1</td><td>-3</td><td>1</td><td>0</td><td>-1</td><td>-1</td><td>-7</td><td>-1</td><td>-5</td><td>0</td></tr>
+<tr><td>H</td><td>-1</td><td>1</td><td>-3</td><td>1</td><td>1</td><td>-2</td><td>-2</td><td>6</td><td>-2</td><td>0</td><td>-2</td><td>-2</td><td>2</td><td>0</td><td>3</td><td>2</td><td>-1</td><td>-1</td><td>-1</td><td>-2</td><td>-3</td><td>-1</td><td>0</td><td>2</td></tr>
+<tr><td>I</td><td>-1</td><td>-2</td><td>-2</td><td>-2</td><td>-2</td><td>1</td><td>-3</td><td>-2</td><td>5</td><td>-2</td><td>2</td><td>2</td><td>-2</td><td>-2</td><td>-2</td><td>-2</td><td>-1</td><td>0</td><td>-1</td><td>4</td><td>-5</td><td>-1</td><td>-1</td><td>-2</td></tr>
+<tr><td>K</td><td>-1</td><td>1</td><td>-5</td><td>0</td><td>0</td><td>-5</td><td>-2</td><td>0</td><td>-2</td><td>5</td><td>-3</td><td>0</td><td>1</td><td>-1</td><td>1</td><td>3</td><td>0</td><td>0</td><td>-1</td><td>-2</td><td>-3</td><td>-1</td><td>-4</td><td>0</td></tr>
+<tr><td>L</td><td>-2</td><td>-3</td><td>-6</td><td>-4</td><td>-3</td><td>2</td><td>-4</td><td>-2</td><td>2</td><td>-3</td><td>6</td><td>4</td><td>-3</td><td>-3</td><td>-2</td><td>-3</td><td>-3</td><td>-2</td><td>-1</td><td>2</td><td>-2</td><td>-1</td><td>-1</td><td>-3</td></tr>
+<tr><td>M</td><td>-1</td><td>-2</td><td>-5</td><td>-3</td><td>-2</td><td>0</td><td>-3</td><td>-2</td><td>2</td><td>0</td><td>4</td><td>6</td><td>-2</td><td>-2</td><td>-1</td><td>0</td><td>-2</td><td>-1</td><td>-1</td><td>2</td><td>-4</td><td>-1</td><td>-2</td><td>-2</td></tr>
+<tr><td>N</td><td>0</td><td>2</td><td>-4</td><td>2</td><td>1</td><td>-3</td><td>0</td><td>2</td><td>-2</td><td>1</td><td>-3</td><td>-2</td><td>2</td><td>0</td><td>1</td><td>0</td><td>1</td><td>0</td><td>0</td><td>-2</td><td>-4</td><td>0</td><td>-2</td><td>1</td></tr>
+<tr><td>P</td><td>1</td><td>-1</td><td>-3</td><td>-1</td><td>-1</td><td>-5</td><td>0</td><td>0</td><td>-2</td><td>-1</td><td>-3</td><td>-2</td><td>0</td><td>6</td><td>0</td><td>0</td><td>1</td><td>0</td><td>-1</td><td>-1</td><td>-6</td><td>-1</td><td>-5</td><td>0</td></tr>
+<tr><td>Q</td><td>0</td><td>1</td><td>-5</td><td>2</td><td>2</td><td>-5</td><td>-1</td><td>3</td><td>-2</td><td>1</td><td>-2</td><td>-1</td><td>1</td><td>0</td><td>4</td><td>1</td><td>-1</td><td>-1</td><td>-1</td><td>-2</td><td>-5</td><td>-1</td><td>-4</td><td>3</td></tr>
+<tr><td>R</td><td>-2</td><td>-1</td><td>-4</td><td>-1</td><td>-1</td><td>-4</td><td>-3</td><td>2</td><td>-2</td><td>3</td><td>-3</td><td>0</td><td>0</td><td>0</td><td>1</td><td>6</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>2</td><td>-1</td><td>-4</td><td>0</td></tr>
+<tr><td>S</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>-3</td><td>1</td><td>-1</td><td>-1</td><td>0</td><td>-3</td><td>-2</td><td>1</td><td>1</td><td>-1</td><td>0</td><td>2</td><td>1</td><td>0</td><td>-1</td><td>-2</td><td>0</td><td>-3</td><td>0</td></tr>
+<tr><td>T</td><td>1</td><td>0</td><td>-2</td><td>0</td><td>0</td><td>-3</td><td>0</td><td>-1</td><td>0</td><td>0</td><td>-2</td><td>-1</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>1</td><td>3</td><td>0</td><td>0</td><td>-5</td><td>0</td><td>-3</td><td>-1</td></tr>
+<tr><td>U</td><td>0</td><td>-1</td><td>-3</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>0</td><td>-1</td><td>-1</td><td>-1</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>-4</td><td>-1</td><td>-2</td><td>-1</td></tr>
+<tr><td>V</td><td>0</td><td>-2</td><td>-2</td><td>-2</td><td>-2</td><td>-1</td><td>-1</td><td>-2</td><td>4</td><td>-2</td><td>2</td><td>2</td><td>-2</td><td>-1</td><td>-2</td><td>-2</td><td>-1</td><td>0</td><td>-1</td><td>4</td><td>-6</td><td>-1</td><td>-2</td><td>-2</td></tr>
+<tr><td>W</td><td>-6</td><td>-5</td><td>-8</td><td>-7</td><td>-7</td><td>0</td><td>-7</td><td>-3</td><td>-5</td><td>-3</td><td>-2</td><td>-4</td><td>-4</td><td>-6</td><td>-5</td><td>2</td><td>-2</td><td>-5</td><td>-4</td><td>-6</td><td>17</td><td>-4</td><td>0</td><td>-6</td></tr>
+<tr><td>X</td><td>0</td><td>-1</td><td>-3</td><td>-1</td><td>-1</td><td>-2</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>-1</td><td>0</td><td>-1</td><td>-1</td><td>-1</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>-4</td><td>-1</td><td>-2</td><td>-1</td></tr>
+<tr><td>Y</td><td>-3</td><td>-3</td><td>0</td><td>-4</td><td>-4</td><td>7</td><td>-5</td><td>0</td><td>-1</td><td>-4</td><td>-1</td><td>-2</td><td>-2</td><td>-5</td><td>-4</td><td>-4</td><td>-3</td><td>-3</td><td>-2</td><td>-2</td><td>0</td><td>-2</td><td>10</td><td>-4</td></tr>
+<tr><td>Z</td><td>0</td><td>2</td><td>-5</td><td>3</td><td>3</td><td>-5</td><td>0</td><td>2</td><td>-2</td><td>0</td><td>-3</td><td>-2</td><td>1</td><td>0</td><td>3</td><td>0</td><td>0</td><td>-1</td><td>-1</td><td>-2</td><td>-6</td><td>-1</td><td>-4</td><td>3</td></tr>
+</table>
+
+<p><strong><a name="simplenucleotide">Simple Nucleotide Substitution</a></strong></br>
+This is an ad-hoc matrix which, in addition to penalising mutations between the common nucleotides (ACGT), includes T/U equivalence in order to allow both DNA and/or RNA.
+In addition, it encodes weak equivalence between R and Y with AG and CTU, respectively, and N is allowed to match any other base weakly. This matrix also includes I (Inosine) and X (Xanthine), but encodes them to weakly match any of (ACGTU), and unfavourably match each other.
+<table border="1">
+<tr><td></td><td>&nbsp;A&nbsp;</td><td>&nbsp;C&nbsp;</td><td>&nbsp;G&nbsp;</td><td>&nbsp;I&nbsp;</td><td>&nbsp;N&nbsp;</td><td>&nbsp;R&nbsp;</td><td>&nbsp;T&nbsp;</td><td>&nbsp;U&nbsp;</td><td>&nbsp;X&nbsp;</td><td>&nbsp;Y&nbsp;</td></tr>
+<tr><td>A</td><td>10</td><td>-8</td><td>-8</td><td>1</td><td>1</td><td>1</td><td>-8</td><td>-8</td><td>1</td><td>-8</td></tr>
+<tr><td>C</td><td>-8</td><td>10</td><td>-8</td><td>1</td><td>1</td><td>-8</td><td>-8</td><td>-8</td><td>1</td><td>1</td></tr>
+<tr><td>G</td><td>-8</td><td>-8</td><td>10</td><td>1</td><td>1</td><td>1</td><td>-8</td><td>-8</td><td>1</td><td>-8</td></tr>
+<tr><td>I</td><td>1</td><td>1</td><td>1</td><td>10</td><td>1</td><td>0</td><td>1</td><td>1</td><td>0</td><td>0</td></tr>
+<tr><td>N</td><td>1</td><td>1</td><td>1</td><td>1</td><td>10</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr>
+<tr><td>R</td><td>1</td><td>-8</td><td>1</td><td>0</td><td>1</td><td>10</td><td>-8</td><td>-8</td><td>0</td><td>-8</td></tr>
+<tr><td>T</td><td>-8</td><td>-8</td><td>-8</td><td>1</td><td>1</td><td>-8</td><td>10</td><td>10</td><td>1</td><td>1</td></tr>
+<tr><td>U</td><td>-8</td><td>-8</td><td>-8</td><td>1</td><td>1</td><td>-8</td><td>10</td><td>10</td><td>1</td><td>1</td></tr>
+<tr><td>X</td><td>1</td><td>1</td><td>1</td><td>0</td><td>1</td><td>0</td><td>1</td><td>1</td><td>10</td><td>0</td></tr>
+<tr><td>Y</td><td>-8</td><td>1</td><td>-8</td><td>0</td><td>1</td><td>-8</td><td>1</td><td>1</td><td>0</td><td>10</td></tr>
+</table>
+<strong><em>This nucleotide matrix was introduced in
+                               Jalview 2.8. If you'd like to improve it - please take a look at <a
+                               href="http://issues.jalview.org/browse/JAL-1027">Issue JAL-1027
+                                       - introduce a nucleotide substitution matrix that supports RNA/DNA
+                                       and ambiguity codes</a>
+               </em></strong>
+               </body>
+</html>
\ No newline at end of file
diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 98b7101..99fc074 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -589,15 +589,15 @@ public class ResidueProperties
   // 
   static final int[][] DNA =
   {
-      { 10, -8, -8, -8, -8, 1,  1, -8,  1,  1, 1 }, // C
-      { -8, 10, -8, -8, 10, 1,  1, -8,  1,  1, 1 }, // T
-      { -8, -8, 10, -8, -8, 1,  1,  1, -8,  1, 1 }, // A
-      { -8, -8, -8, 10, -8, 1,  1,  1, -8,  1, 1 }, // G
-      { -8, 10, -8, -8, 10, 1,  1, -8,  1,  1, 1 }, // U
+      { 10, -8, -8, -8, -8, 1,  1,  1, -8,  1, 1 }, // A
+      { -8, 10, -8, -8, -8, 1,  1, -8,  1,  1, 1 }, // C
+      { -8, -8, 10, -8, -8, 1,  1,  1, -8,  1, 1 }, // G
+      { -8, -8, -8, 10, 10, 1,  1, -8,  1,  1, 1 }, // T
+      { -8, -8, -8, 10, 10, 1,  1, -8,  1,  1, 1 }, // U
       {  1,  1,  1,  1,  1, 10, 0,  0,  0,  1, 1 }, // I
       {  1,  1,  1,  1,  1, 0, 10,  0,  0,  1, 1 }, // X
-      { -8, -8,  1,  1, -8, 0,  0, 10,  0,  1, 1 }, // R
-      {  1,  1, -8, -8,  1, 0,  0,  0, 10,  1, 1 }, // Y
+      {  1, -8,  1, -8, -8, 0,  0, 10, -8,  1, 1 }, // R
+      { -8,  1, -8,  1,  1, 0,  0, -8, 10,  1, 1 }, // Y
       {  1,  1,  1,  1,  1, 1,  1,  1,  1, 10, 1 }, // N
       {  1,  1,  1,  1,  1, 1,  1,  1,  1,  1, 1 }, // -
   };