-<html>\r
-<head><title>Alignment Conservation Annotation</title></head>\r
-<body><p><strong>Alignment Conservation Annotation</strong></p>\r
-<p>This is an automatically calculated quantitative alignment\r
-annotation which measures the number of conserved physico-chemical\r
-properties conserved for each column of the alignment. Its calculation\r
-is based on the one used in\r
- the AMAS method of multiple sequence alignment analysis :<br>\r
-<ul>Livingstone\r
- C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy \r
- for the Hierarchical Analysis of Residue Conservation.<em>CABIOS</em> Vol. <b>9</b>\r
- No. 6 (745-756)).\r
-</ul>\r
-</p>\r
-<p>Conservation is measured as a numerical index reflecting the conservation of \r
- <a href="../misc/aaproperties.html">physico-chemical \r
- properties</a> in the alignment: Identities score highest, and the next most \r
- conserved group contain substitutions to amino acids lying in the same physico-chemical \r
- class.</p>\r
-\r
-<p><em>Colouring an alignment by conservation</em><br>\r
-Conservation scores can be used to colour an alignment. This is\r
-explained further in the help page for <a\r
-href="../colourSchemes/conservation.html">conservation colouring</a>.\r
-</p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Alignment Conservation Annotation</title>
+</head>
+<body>
+ <p>
+ <strong>Alignment Conservation Annotation</strong>
+ </p>
+ <p>
+ This is an automatically calculated quantitative alignment
+ annotation which measures the number of conserved physico-chemical
+ properties conserved for each column of the alignment. Its
+ calculation is based on the one used in the AMAS method of multiple
+ sequence alignment analysis :<br>
+ <ul>
+ Livingstone C.D. and Barton G.J. (1993), Protein Sequence
+ Alignments: A Strategy 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>
+ Mousing over a conservation histogram reveals a tooltip which
+ contains a series of symbols corresponding to the physicochemical
+ properties that are conserved amongst the amino acids observed at
+ each position. In these tooltips, the presence of <em>!</em> implies
+ that the lack of a particular physicochemical property is conserved
+ (e.g. !proline).
+ </p>
+ <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>.
+ </p>
+</body>
+</html>