From cafa2071799c16922a85b8637e33e6331e054f35 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 24 May 2012 11:58:53 +0100
Subject: [PATCH] JAL-1107 - documentation explaining '*' and '+' in the
 conservation histogram.

---
 help/html/calculations/conservation.html |    9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/help/html/calculations/conservation.html b/help/html/calculations/conservation.html
index 7c5953f..bd4a625 100755
--- a/help/html/calculations/conservation.html
+++ b/help/html/calculations/conservation.html
@@ -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>.
-- 
1.7.10.2