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<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, 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
+ Substitution</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> A </td><td> B </td><td> C </td><td> D </td><td> E </td><td> F </td><td> G </td><td> H </td><td> I </td><td> K </td><td> L </td><td> M </td><td> N </td><td> P </td><td> Q </td><td> R </td><td> S </td><td> T </td><td> U </td><td> V </td><td> W </td><td> X </td><td> Y </td><td> Z </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> A </td><td> B </td><td> C </td><td> D </td><td> E </td><td> F </td><td> G </td><td> H </td><td> I </td><td> K </td><td> L </td><td> M </td><td> N </td><td> P </td><td> Q </td><td> R </td><td> S </td><td> T </td><td> U </td><td> V </td><td> W </td><td> X </td><td> Y </td><td> Z </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> A </td>
+ <td> B </td>
+ <td> C </td>
+ <td> D </td>
+ <td> E </td>
+ <td> F </td>
+ <td> G </td>
+ <td> H </td>
+ <td> I </td>
+ <td> K </td>
+ <td> L </td>
+ <td> M </td>
+ <td> N </td>
+ <td> P </td>
+ <td> Q </td>
+ <td> R </td>
+ <td> S </td>
+ <td> T </td>
+ <td> U </td>
+ <td> V </td>
+ <td> W </td>
+ <td> X </td>
+ <td> Y </td>
+ <td> Z </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> A </td>
+ <td> B </td>
+ <td> C </td>
+ <td> D </td>
+ <td> E </td>
+ <td> F </td>
+ <td> G </td>
+ <td> H </td>
+ <td> I </td>
+ <td> K </td>
+ <td> L </td>
+ <td> M </td>
+ <td> N </td>
+ <td> P </td>
+ <td> Q </td>
+ <td> R </td>
+ <td> S </td>
+ <td> T </td>
+ <td> U </td>
+ <td> V </td>
+ <td> W </td>
+ <td> X </td>
+ <td> Y </td>
+ <td> Z </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> A </td><td> C </td><td> G </td><td> I </td><td> N </td><td> R </td><td> T </td><td> U </td><td> X </td><td> Y </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> A </td>
+ <td> C </td>
+ <td> G </td>
+ <td> I </td>
+ <td> N </td>
+ <td> R </td>
+ <td> T </td>
+ <td> U </td>
+ <td> X </td>
+ <td> Y </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).
</li> -->
-</ul>
- </body>
+ </ul>
+</body>
</html>