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JAL-2089 patch broken merge to master for Release 2.10.0b1
[jalview.git] / help / html / calculations / scorematrices.html
diff --git a/help/html/calculations/scorematrices.html b/help/html/calculations/scorematrices.html
index 231157a..5fbbc19 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 2.9.0b1)
- * 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>