<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
- *
+ * 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/>.
--->
+ * 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>
+ <strong>Colouring an alignment by conservation</strong><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>
+ <p>
+ <strong>Group conservation</strong><br> If sequence groups have
+ been defined, then selecting option 'Group Conservation' in the <a
+ href="../menus/alwannotation.html">Annotations menu</a> will
+ result in Conservation being calculated for each group, as well as
+ the alignment as a whole.
+ </p>
+</body>
+</html>