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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, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
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>.
git://source.jalview.org / jalview.git / blobdiff