3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
4 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
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19 <head><title>Alignment Conservation Annotation</title></head>
20 <body><p><strong>Alignment Conservation Annotation</strong></p>
21 <p>This is an automatically calculated quantitative alignment
22 annotation which measures the number of conserved physico-chemical
23 properties conserved for each column of the alignment. Its calculation
24 is based on the one used in
25 the AMAS method of multiple sequence alignment analysis :<br>
27 C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy
28 for the Hierarchical Analysis of Residue Conservation.<em>CABIOS</em> Vol. <b>9</b>
32 <p>Conservation is measured as a numerical index reflecting the conservation of
33 <a href="../misc/aaproperties.html">physico-chemical
34 properties</a> in the alignment: Identities score highest, and the next most
35 conserved group contain substitutions to amino acids lying in the same physico-chemical
38 <p><em>Colouring an alignment by conservation</em><br>
39 Conservation scores can be used to colour an alignment. This is
40 explained further in the help page for <a
41 href="../colourSchemes/conservation.html">conservation colouring</a>.