X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fscorematrices.html;h=cb07a498ad4a1451542ddc06a1060d9238019587;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=9a40e69c76982521f2ed42d4d43dd88b266d88de;hpb=a86681109f3b9be838ae3fb2dd9d6db544be4bce;p=jalview.git

diff --git a/help/html/calculations/scorematrices.html b/help/html/calculations/scorematrices.html
index 9a40e69..cb07a49 100644
--- a/help/html/calculations/scorematrices.html
+++ b/help/html/calculations/scorematrices.html
@@ -1,4 +1,24 @@
 <html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
 <head>
 <title>Substitution matrices in Jalview</title>
 </head>
@@ -7,9 +27,10 @@
 <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>
+<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>
 
 <p><strong><a name="blosum62"></a>BLOSUM62</strong><br/>
@@ -41,6 +62,8 @@
 <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>
@@ -69,7 +92,7 @@
 <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>
+<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">
@@ -91,5 +114,100 @@ In addition, it encodes weak equivalence between R and Y with AG and CTU, respec
 					- 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).
+
+<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>20</td><td>0</td><td>18</td><td>10</td><td>8</td><td>14</td><td>20</td><td>8</td><td>14</td><td>10</td><td>14</td><td>16</td><td>14</td><td>14</td><td>12</td><td>8</td><td>16</td><td>14</td><td>2</td><td>16</td><td>12</td><td>2</td><td>12</td><td>0</td></tr>
+<tr><td>B</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr>
+<tr><td>C</td><td>18</td><td>0</td><td>18</td><td>12</td><td>10</td><td>16</td><td>18</td><td>10</td><td>16</td><td>12</td><td>16</td><td>18</td><td>16</td><td>16</td><td>14</td><td>10</td><td>14</td><td>16</td><td>2</td><td>18</td><td>14</td><td>2</td><td>14</td><td>0</td></tr>
+<tr><td>D</td><td>10</td><td>0</td><td>12</td><td>18</td><td>18</td><td>8</td><td>10</td><td>10</td><td>8</td><td>12</td><td>8</td><td>10</td><td>16</td><td>12</td><td>14</td><td>14</td><td>14</td><td>16</td><td>2</td><td>10</td><td>10</td><td>2</td><td>10</td><td>0</td></tr>
+<tr><td>E</td><td>8</td><td>0</td><td>10</td><td>18</td><td>14</td><td>10</td><td>8</td><td>12</td><td>10</td><td>14</td><td>10</td><td>12</td><td>14</td><td>10</td><td>16</td><td>16</td><td>12</td><td>14</td><td>2</td><td>8</td><td>12</td><td>2</td><td>12</td><td>0</td></tr>
+<tr><td>F</td><td>14</td><td>0</td><td>16</td><td>8</td><td>10</td><td>18</td><td>14</td><td>14</td><td>16</td><td>12</td><td>16</td><td>18</td><td>12</td><td>12</td><td>14</td><td>10</td><td>10</td><td>12</td><td>2</td><td>14</td><td>18</td><td>2</td><td>18</td><td>0</td></tr>
+<tr><td>G</td><td>20</td><td>0</td><td>18</td><td>10</td><td>8</td><td>14</td><td>16</td><td>8</td><td>14</td><td>10</td><td>14</td><td>16</td><td>14</td><td>14</td><td>12</td><td>8</td><td>16</td><td>14</td><td>2</td><td>16</td><td>12</td><td>2</td><td>12</td><td>0</td></tr>
+<tr><td>H</td><td>8</td><td>0</td><td>10</td><td>10</td><td>12</td><td>14</td><td>8</td><td>18</td><td>10</td><td>18</td><td>10</td><td>12</td><td>10</td><td>6</td><td>12</td><td>16</td><td>8</td><td>10</td><td>4</td><td>8</td><td>16</td><td>4</td><td>16</td><td>0</td></tr>
+<tr><td>I</td><td>14</td><td>0</td><td>16</td><td>8</td><td>10</td><td>16</td><td>14</td><td>10</td><td>20</td><td>12</td><td>20</td><td>18</td><td>12</td><td>12</td><td>14</td><td>10</td><td>10</td><td>12</td><td>2</td><td>18</td><td>14</td><td>2</td><td>14</td><td>0</td></tr>
+<tr><td>K</td><td>10</td><td>0</td><td>12</td><td>12</td><td>14</td><td>12</td><td>10</td><td>18</td><td>12</td><td>14</td><td>12</td><td>14</td><td>12</td><td>8</td><td>14</td><td>18</td><td>10</td><td>12</td><td>4</td><td>10</td><td>14</td><td>4</td><td>14</td><td>0</td></tr>
+<tr><td>L</td><td>14</td><td>0</td><td>16</td><td>8</td><td>10</td><td>16</td><td>14</td><td>10</td><td>20</td><td>12</td><td>18</td><td>18</td><td>12</td><td>12</td><td>14</td><td>10</td><td>10</td><td>12</td><td>2</td><td>18</td><td>14</td><td>2</td><td>14</td><td>0</td></tr>
+<tr><td>M</td><td>16</td><td>0</td><td>18</td><td>10</td><td>12</td><td>18</td><td>16</td><td>12</td><td>18</td><td>14</td><td>18</td><td>18</td><td>14</td><td>14</td><td>16</td><td>12</td><td>12</td><td>14</td><td>2</td><td>16</td><td>16</td><td>2</td><td>16</td><td>0</td></tr>
+<tr><td>N</td><td>14</td><td>0</td><td>16</td><td>16</td><td>14</td><td>12</td><td>14</td><td>10</td><td>12</td><td>12</td><td>12</td><td>14</td><td>20</td><td>16</td><td>18</td><td>14</td><td>18</td><td>20</td><td>2</td><td>14</td><td>14</td><td>2</td><td>14</td><td>0</td></tr>
+<tr><td>P</td><td>14</td><td>0</td><td>16</td><td>12</td><td>10</td><td>12</td><td>14</td><td>6</td><td>12</td><td>8</td><td>12</td><td>14</td><td>16</td><td>16</td><td>14</td><td>10</td><td>14</td><td>16</td><td>0</td><td>14</td><td>10</td><td>0</td><td>10</td><td>0</td></tr>
+<tr><td>Q</td><td>12</td><td>0</td><td>14</td><td>14</td><td>16</td><td>14</td><td>12</td><td>12</td><td>14</td><td>14</td><td>14</td><td>16</td><td>18</td><td>14</td><td>18</td><td>16</td><td>16</td><td>18</td><td>2</td><td>12</td><td>16</td><td>2</td><td>16</td><td>0</td></tr>
+<tr><td>R</td><td>8</td><td>0</td><td>10</td><td>14</td><td>16</td><td>10</td><td>8</td><td>16</td><td>10</td><td>18</td><td>10</td><td>12</td><td>14</td><td>10</td><td>16</td><td>18</td><td>12</td><td>14</td><td>2</td><td>8</td><td>12</td><td>2</td><td>12</td><td>0</td></tr>
+<tr><td>S</td><td>16</td><td>0</td><td>14</td><td>14</td><td>12</td><td>10</td><td>16</td><td>8</td><td>10</td><td>10</td><td>10</td><td>12</td><td>18</td><td>14</td><td>16</td><td>12</td><td>18</td><td>18</td><td>2</td><td>12</td><td>12</td><td>2</td><td>12</td><td>0</td></tr>
+<tr><td>T</td><td>14</td><td>0</td><td>16</td><td>16</td><td>14</td><td>12</td><td>14</td><td>10</td><td>12</td><td>12</td><td>12</td><td>14</td><td>20</td><td>16</td><td>18</td><td>14</td><td>18</td><td>14</td><td>2</td><td>14</td><td>14</td><td>2</td><td>14</td><td>0</td></tr>
+<tr><td>U</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>4</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>4</td><td>0</td><td>4</td><td>0</td></tr>
+<tr><td>V</td><td>16</td><td>0</td><td>18</td><td>10</td><td>8</td><td>14</td><td>16</td><td>8</td><td>18</td><td>10</td><td>18</td><td>16</td><td>14</td><td>14</td><td>12</td><td>8</td><td>12</td><td>14</td><td>2</td><td>2</td><td>12</td><td>2</td><td>12</td><td>0</td></tr>
+<tr><td>W</td><td>12</td><td>0</td><td>14</td><td>10</td><td>12</td><td>18</td><td>12</td><td>16</td><td>14</td><td>14</td><td>14</td><td>16</td><td>14</td><td>10</td><td>16</td><td>12</td><td>12</td><td>14</td><td>4</td><td>12</td><td>20</td><td>4</td><td>20</td><td>0</td></tr>
+<tr><td>X</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>4</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>4</td><td>0</td><td>4</td><td>0</td></tr>
+<tr><td>Y</td><td>12</td><td>0</td><td>14</td><td>10</td><td>12</td><td>18</td><td>12</td><td>16</td><td>14</td><td>14</td><td>14</td><td>16</td><td>14</td><td>10</td><td>16</td><td>12</td><td>12</td><td>14</td><td>4</td><td>12</td><td>20</td><td>4</td><td>12</td><td>0</td></tr>
+<tr><td>Z</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr>
+</table>
+
+<li><em>Conservation Pos</em><br>Count number of properties that amino acids both have in common.
+
+<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>6</td><td>0</td><td>4</td><td>2</td><td>0</td><td>2</td><td>6</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td><td>0</td><td>4</td><td>2</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>B</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr>
+<tr><td>C</td><td>4</td><td>0</td><td>4</td><td>2</td><td>0</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td><td>0</td><td>2</td><td>2</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>D</td><td>2</td><td>0</td><td>2</td><td>6</td><td>6</td><td>0</td><td>2</td><td>4</td><td>0</td><td>4</td><td>0</td><td>0</td><td>4</td><td>2</td><td>2</td><td>4</td><td>4</td><td>4</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>E</td><td>0</td><td>0</td><td>0</td><td>6</td><td>4</td><td>0</td><td>0</td><td>4</td><td>0</td><td>4</td><td>0</td><td>0</td><td>2</td><td>0</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>F</td><td>2</td><td>0</td><td>2</td><td>0</td><td>0</td><td>4</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>2</td><td>2</td><td>4</td><td>2</td><td>4</td><td>0</td></tr>
+<tr><td>G</td><td>6</td><td>0</td><td>4</td><td>2</td><td>0</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td><td>0</td><td>4</td><td>2</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>H</td><td>2</td><td>0</td><td>2</td><td>4</td><td>4</td><td>4</td><td>2</td><td>8</td><td>2</td><td>8</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>6</td><td>2</td><td>2</td><td>4</td><td>2</td><td>6</td><td>4</td><td>6</td><td>0</td></tr>
+<tr><td>I</td><td>2</td><td>0</td><td>2</td><td>0</td><td>0</td><td>2</td><td>2</td><td>2</td><td>4</td><td>2</td><td>4</td><td>2</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>K</td><td>2</td><td>0</td><td>2</td><td>4</td><td>4</td><td>2</td><td>2</td><td>8</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>6</td><td>2</td><td>2</td><td>4</td><td>2</td><td>4</td><td>4</td><td>4</td><td>0</td></tr>
+<tr><td>L</td><td>2</td><td>0</td><td>2</td><td>0</td><td>0</td><td>2</td><td>2</td><td>2</td><td>4</td><td>2</td><td>4</td><td>2</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>M</td><td>2</td><td>0</td><td>2</td><td>0</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>N</td><td>2</td><td>0</td><td>2</td><td>4</td><td>2</td><td>0</td><td>2</td><td>2</td><td>0</td><td>2</td><td>0</td><td>0</td><td>4</td><td>2</td><td>2</td><td>2</td><td>4</td><td>4</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>P</td><td>2</td><td>0</td><td>2</td><td>2</td><td>0</td><td>0</td><td>2</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>2</td><td>2</td><td>0</td><td>0</td><td>2</td><td>2</td><td>0</td><td>2</td><td>0</td><td>0</td><td>0</td><td>0</td></tr>
+<tr><td>Q</td><td>0</td><td>0</td><td>0</td><td>2</td><td>2</td><td>0</td><td>0</td><td>2</td><td>0</td><td>2</td><td>0</td><td>0</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>R</td><td>0</td><td>0</td><td>0</td><td>4</td><td>4</td><td>0</td><td>0</td><td>6</td><td>0</td><td>6</td><td>0</td><td>0</td><td>2</td><td>0</td><td>2</td><td>6</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>S</td><td>4</td><td>0</td><td>2</td><td>4</td><td>2</td><td>0</td><td>4</td><td>2</td><td>0</td><td>2</td><td>0</td><td>0</td><td>4</td><td>2</td><td>2</td><td>2</td><td>4</td><td>4</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>T</td><td>2</td><td>0</td><td>2</td><td>4</td><td>2</td><td>0</td><td>2</td><td>2</td><td>0</td><td>2</td><td>0</td><td>0</td><td>4</td><td>2</td><td>2</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>U</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>4</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>4</td><td>0</td><td>4</td><td>0</td></tr>
+<tr><td>V</td><td>4</td><td>0</td><td>4</td><td>2</td><td>0</td><td>2</td><td>4</td><td>2</td><td>4</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td></tr>
+<tr><td>W</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>4</td><td>2</td><td>6</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>4</td><td>2</td><td>6</td><td>4</td><td>6</td><td>0</td></tr>
+<tr><td>X</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>2</td><td>4</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>4</td><td>0</td><td>4</td><td>0</td></tr>
+<tr><td>Y</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>4</td><td>2</td><td>6</td><td>2</td><td>4</td><td>2</td><td>2</td><td>2</td><td>0</td><td>2</td><td>2</td><td>2</td><td>2</td><td>4</td><td>2</td><td>6</td><td>4</td><td>4</td><td>0</td></tr>
+<tr><td>Z</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr>
+</table>
+
+</li>
+<li>
+<em>Conservation EnhPos</em><br>Distinguish amino acids based on properties they have in common or lack, emphasising those they have in common.
+
+<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>16</td><td>0</td><td>13</td><td>7</td><td>4</td><td>9</td><td>16</td><td>6</td><td>9</td><td>7</td><td>9</td><td>10</td><td>9</td><td>9</td><td>6</td><td>4</td><td>12</td><td>9</td><td>3</td><td>12</td><td>8</td><td>3</td><td>8</td><td>0</td></tr>
+<tr><td>B</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr>
+<tr><td>C</td><td>13</td><td>0</td><td>13</td><td>8</td><td>5</td><td>10</td><td>13</td><td>7</td><td>10</td><td>8</td><td>10</td><td>11</td><td>10</td><td>10</td><td>7</td><td>5</td><td>9</td><td>10</td><td>3</td><td>13</td><td>9</td><td>3</td><td>9</td><td>0</td></tr>
+<tr><td>D</td><td>7</td><td>0</td><td>8</td><td>15</td><td>15</td><td>4</td><td>7</td><td>9</td><td>4</td><td>10</td><td>4</td><td>5</td><td>12</td><td>8</td><td>9</td><td>11</td><td>11</td><td>12</td><td>3</td><td>7</td><td>7</td><td>3</td><td>7</td><td>0</td></tr>
+<tr><td>E</td><td>4</td><td>0</td><td>5</td><td>15</td><td>11</td><td>5</td><td>4</td><td>10</td><td>5</td><td>11</td><td>5</td><td>6</td><td>9</td><td>5</td><td>10</td><td>12</td><td>8</td><td>9</td><td>3</td><td>4</td><td>8</td><td>3</td><td>8</td><td>0</td></tr>
+<tr><td>F</td><td>9</td><td>0</td><td>10</td><td>4</td><td>5</td><td>13</td><td>9</td><td>11</td><td>10</td><td>8</td><td>10</td><td>11</td><td>6</td><td>6</td><td>7</td><td>5</td><td>5</td><td>6</td><td>3</td><td>9</td><td>13</td><td>3</td><td>13</td><td>0</td></tr>
+<tr><td>G</td><td>16</td><td>0</td><td>13</td><td>7</td><td>4</td><td>9</td><td>12</td><td>6</td><td>9</td><td>7</td><td>9</td><td>10</td><td>9</td><td>9</td><td>6</td><td>4</td><td>12</td><td>9</td><td>3</td><td>12</td><td>8</td><td>3</td><td>8</td><td>0</td></tr>
+<tr><td>H</td><td>6</td><td>0</td><td>7</td><td>9</td><td>10</td><td>11</td><td>6</td><td>17</td><td>7</td><td>17</td><td>7</td><td>8</td><td>7</td><td>3</td><td>8</td><td>14</td><td>6</td><td>7</td><td>6</td><td>6</td><td>14</td><td>6</td><td>14</td><td>0</td></tr>
+<tr><td>I</td><td>9</td><td>0</td><td>10</td><td>4</td><td>5</td><td>10</td><td>9</td><td>7</td><td>14</td><td>8</td><td>14</td><td>11</td><td>6</td><td>6</td><td>7</td><td>5</td><td>5</td><td>6</td><td>3</td><td>13</td><td>9</td><td>3</td><td>9</td><td>0</td></tr>
+<tr><td>K</td><td>7</td><td>0</td><td>8</td><td>10</td><td>11</td><td>8</td><td>7</td><td>17</td><td>8</td><td>11</td><td>8</td><td>9</td><td>8</td><td>4</td><td>9</td><td>15</td><td>7</td><td>8</td><td>6</td><td>7</td><td>11</td><td>6</td><td>11</td><td>0</td></tr>
+<tr><td>L</td><td>9</td><td>0</td><td>10</td><td>4</td><td>5</td><td>10</td><td>9</td><td>7</td><td>14</td><td>8</td><td>13</td><td>11</td><td>6</td><td>6</td><td>7</td><td>5</td><td>5</td><td>6</td><td>3</td><td>13</td><td>9</td><td>3</td><td>9</td><td>0</td></tr>
+<tr><td>M</td><td>10</td><td>0</td><td>11</td><td>5</td><td>6</td><td>11</td><td>10</td><td>8</td><td>11</td><td>9</td><td>11</td><td>11</td><td>7</td><td>7</td><td>8</td><td>6</td><td>6</td><td>7</td><td>3</td><td>10</td><td>10</td><td>3</td><td>10</td><td>0</td></tr>
+<tr><td>N</td><td>9</td><td>0</td><td>10</td><td>12</td><td>9</td><td>6</td><td>9</td><td>7</td><td>6</td><td>8</td><td>6</td><td>7</td><td>14</td><td>10</td><td>11</td><td>9</td><td>13</td><td>14</td><td>3</td><td>9</td><td>9</td><td>3</td><td>9</td><td>0</td></tr>
+<tr><td>P</td><td>9</td><td>0</td><td>10</td><td>8</td><td>5</td><td>6</td><td>9</td><td>3</td><td>6</td><td>4</td><td>6</td><td>7</td><td>10</td><td>10</td><td>7</td><td>5</td><td>9</td><td>10</td><td>0</td><td>9</td><td>5</td><td>0</td><td>5</td><td>0</td></tr>
+<tr><td>Q</td><td>6</td><td>0</td><td>7</td><td>9</td><td>10</td><td>7</td><td>6</td><td>8</td><td>7</td><td>9</td><td>7</td><td>8</td><td>11</td><td>7</td><td>11</td><td>10</td><td>10</td><td>11</td><td>3</td><td>6</td><td>10</td><td>3</td><td>10</td><td>0</td></tr>
+<tr><td>R</td><td>4</td><td>0</td><td>5</td><td>11</td><td>12</td><td>5</td><td>4</td><td>14</td><td>5</td><td>15</td><td>5</td><td>6</td><td>9</td><td>5</td><td>10</td><td>15</td><td>8</td><td>9</td><td>3</td><td>4</td><td>8</td><td>3</td><td>8</td><td>0</td></tr>
+<tr><td>S</td><td>12</td><td>0</td><td>9</td><td>11</td><td>8</td><td>5</td><td>12</td><td>6</td><td>5</td><td>7</td><td>5</td><td>6</td><td>13</td><td>9</td><td>10</td><td>8</td><td>13</td><td>13</td><td>3</td><td>8</td><td>8</td><td>3</td><td>8</td><td>0</td></tr>
+<tr><td>T</td><td>9</td><td>0</td><td>10</td><td>12</td><td>9</td><td>6</td><td>9</td><td>7</td><td>6</td><td>8</td><td>6</td><td>7</td><td>14</td><td>10</td><td>11</td><td>9</td><td>13</td><td>9</td><td>3</td><td>9</td><td>9</td><td>3</td><td>9</td><td>0</td></tr>
+<tr><td>U</td><td>3</td><td>0</td><td>3</td><td>3</td><td>3</td><td>3</td><td>3</td><td>6</td><td>3</td><td>6</td><td>3</td><td>3</td><td>3</td><td>0</td><td>3</td><td>3</td><td>3</td><td>3</td><td>0</td><td>3</td><td>6</td><td>0</td><td>6</td><td>0</td></tr>
+<tr><td>V</td><td>12</td><td>0</td><td>13</td><td>7</td><td>4</td><td>9</td><td>12</td><td>6</td><td>13</td><td>7</td><td>13</td><td>10</td><td>9</td><td>9</td><td>6</td><td>4</td><td>8</td><td>9</td><td>3</td><td>3</td><td>8</td><td>3</td><td>8</td><td>0</td></tr>
+<tr><td>W</td><td>8</td><td>0</td><td>9</td><td>7</td><td>8</td><td>13</td><td>8</td><td>14</td><td>9</td><td>11</td><td>9</td><td>10</td><td>9</td><td>5</td><td>10</td><td>8</td><td>8</td><td>9</td><td>6</td><td>8</td><td>16</td><td>6</td><td>16</td><td>0</td></tr>
+<tr><td>X</td><td>3</td><td>0</td><td>3</td><td>3</td><td>3</td><td>3</td><td>3</td><td>6</td><td>3</td><td>6</td><td>3</td><td>3</td><td>3</td><td>0</td><td>3</td><td>3</td><td>3</td><td>3</td><td>0</td><td>3</td><td>6</td><td>0</td><td>6</td><td>0</td></tr>
+<tr><td>Y</td><td>8</td><td>0</td><td>9</td><td>7</td><td>8</td><td>13</td><td>8</td><td>14</td><td>9</td><td>11</td><td>9</td><td>10</td><td>9</td><td>5</td><td>10</td><td>8</td><td>8</td><td>9</td><td>6</td><td>8</td><td>16</td><td>6</td><td>8</td><td>0</td></tr>
+<tr><td>Z</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td></tr>
+</table>
+
+
+</li> -->
+</ul>
 		</body>
-</html>
\ No newline at end of file
+</html>

	A	B	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	U	V	W	X	Y	Z
A	2	0	-2	0	0	-3	1	-1	-1	-1	-2	-1	0	1	0	-2	1	1	0	0	-6	0	-3	0
Z	0	2	-5	3	3	-5	0	2	-2	0	-3	-2	1	0	3	0	0	-1	-1	-2	-6	-1	-4	3