X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fscorematrices.html;h=5fbbc194f2dde467cf88aad0e748c9d188dd40c7;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=231157a30fcd208a8ca35fb76b7fa5c19fcc1ac5;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git

diff --git a/help/html/calculations/scorematrices.html b/help/html/calculations/scorematrices.html
index 231157a..5fbbc19 100644
--- 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 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -33,7 +33,8 @@
       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>
+        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>
@@ -721,9 +722,10 @@
     <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>
+      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>
@@ -1559,8 +1561,8 @@
   </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
+      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>
