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JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob
[jalview.git] / help / html / calculations / scorematrices.html
diff --git a/help/html/calculations/scorematrices.html b/help/html/calculations/scorematrices.html
index 5c4a498..8a1181d 100644 (file)
--- a/help/html/calculations/scorematrices.html
+++ b/help/html/calculations/scorematrices.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -23,99 +23,1548 @@
 <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, and (since 2.8.1) is available for Tree and PCA calculations.</li>
-<li><a href="#simplenucleotide">Simple Nucleotide Substition</a> is a (fairly) arbitrary DNA/RNA substitution matrix.</li>
-<!--  <li><a href="#conservation">Conservation Matrices</a> A range of matrices for distinguishing amino-acids by physicochemical property conservation.
+  <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, and (since 2.8.1) is available for Tree and PCA
+      calculations.</li>
+    <li><a href="#simplenucleotide">Simple Nucleotide
+        Substition</a> is a (fairly) arbitrary DNA/RNA substitution matrix.</li>
+    <!--  <li><a href="#conservation">Conservation Matrices</a> A range of matrices for distinguishing amino-acids by physicochemical property conservation.
 </li> -->
-</ul>
+  </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/>
-<em><strong>P</strong>ercentage <strong>A</strong>ccepted <strong>M</strong>utation matrix. PAM250 estimates substitutions after 250% of sites have changed (each site can be mutated multple times).<br/>
-Jalview 2.8.1 introduced support for PAM250 based <a href="../calculations/pca.html">PCA</a> and <a href="../calculations/trees.html">tree</a> calculations.</em>
-<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="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 /> <em><strong>P</strong>ercentage
+      <strong>A</strong>ccepted <strong>M</strong>utation matrix. PAM250
+      estimates substitutions after 250% of sites have changed (each
+      site can be mutated multple times).<br /> Jalview 2.8.1 introduced
+      support for PAM250 based <a href="../calculations/pca.html">PCA</a>
+      and <a href="../calculations/tree.html">tree</a> calculations.</em>
+  <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>
-               </p>
-<!--  <p><strong><a name="conservation">Physicochemical property conservation</a></strong><br>
+  <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>
+  </p>
+  <!--  <p><strong><a name="conservation">Physicochemical property conservation</a></strong><br>
 Three different matrices are provided which reflect differences in physicochemical properties for different amino-acids.
 <ul><li><em>Conservation Both</em><br>Matrix elements count number of properties shared, and number of properties that both amino-acids *do not* have (e.g. hydrophobic and not polar).
 
@@ -208,6 +1657,6 @@ Three different matrices are provided which reflect differences in physicochemic
 
 
 </li> -->
-</ul>
-               </body>
+  </ul>
+</body>
 </html>