X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fcalculations%2Fconservation.html;h=bd4a625aec7b80e3a14976c417543515e7604be8;hb=96f3f9ed47f4d7e5c094a49c5655fa946a186440;hp=ebba3ab15b8fedaba1854b9ee5e390b6645b3967;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/help/html/calculations/conservation.html b/help/html/calculations/conservation.html
index ebba3ab..bd4a625 100755
--- a/help/html/calculations/conservation.html
+++ b/help/html/calculations/conservation.html
@@ -1,7 +1,7 @@
 <html>
 <!--
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -28,14 +28,21 @@ is based on the one used in
   for the Hierarchical Analysis of Residue Conservation.<em>CABIOS</em> Vol. <b>9</b>
   No. 6 (745-756)).
 </ul>
+<em><a href="http://www.compbio.dundee.ac.uk/papers/amas/amas3d.html">View an HTML version of the paper</a></em>
 </p>
 <p>Conservation is measured as a numerical index reflecting the conservation of 
   <a href="../misc/aaproperties.html">physico-chemical 
   properties</a> in the alignment: Identities score highest, and the next most 
   conserved group contain substitutions to amino acids lying in the same physico-chemical 
   class.</p>
+	<p>Conservation is visualised on the alignment or a sequence group
+		as a histogram giving the score for each column. Conserved columns are
+		indicated by '*' (score of 11 with default amino acid property
+		grouping), and columns with mutations where all properties are
+		conserved are marked with a '+' (score of 10, indicating all
+		properties are conserved).</p>
 
-<p><em>Colouring an alignment by conservation</em><br>
+	<p><em>Colouring an alignment by conservation</em><br>
 Conservation scores can be used to colour an alignment.  This is
 explained further in the help page for <a
 href="../colourSchemes/conservation.html">conservation colouring</a>.
