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- * 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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+<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>
+</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><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>
git://source.jalview.org / jalview.git / blobdiff