X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fscorematrices.html;h=5c4a498f781ac8e00391ab57519e7bf90d9bca42;hb=91e9ddff22dd9406d8784b8a91f03d7b94b4a180;hp=3858b53411fe3e42ae24ffcacacd021c15a8778a;hpb=d5538cea7610ca0658449f0bcdb8a7063c3c90fe;p=jalview.git

diff --git a/help/html/calculations/scorematrices.html b/help/html/calculations/scorematrices.html
index 3858b53..5c4a498 100644
--- a/help/html/calculations/scorematrices.html
+++ b/help/html/calculations/scorematrices.html
@@ -1,22 +1,24 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * 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.
+ * 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/>.
+ * 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>
@@ -25,7 +27,7 @@
 <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="#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> -->
@@ -60,6 +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>
