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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
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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>
-<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>
-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>
+<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>
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