-<html>
-<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 physico-chemical properties 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>
+<html>\r
+<head><title>Alignment Conservation Annotation</title></head>\r
+<body><p><strong>Alignment Conservation Annotation</strong></p>\r
+<p>This is an automatically calculated quantitative alignment\r
+annotation which measures the number of conserved physico-chemical\r
+properties conserved for each column of the alignment. Its calculation\r
+is based on the one used in\r
+ the AMAS method of multiple sequence alignment analysis :<br>\r
+<ul>Livingstone\r
+ C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy \r
+ for the Hierarchical Analysis of Residue Conservation.<em>CABIOS</em> Vol. <b>9</b>\r
+ No. 6 (745-756)).\r
+</ul>\r
+</p>\r
+<p>Conservation is measured as a numerical index reflecting the conservation of \r
+ <a href="../misc/aaproperties.html">physico-chemical \r
+ properties</a> in the alignment: Identities score highest, and the next most \r
+ conserved group contain substitutions to amino acids lying in the same physico-chemical \r
+ class.</p>\r
+\r
+<p><em>Colouring an alignment by conservation</em><br>\r
+Conservation scores can be used to colour an alignment. This is\r
+explained further in the help page for <a\r
+href="../colourSchemes/conservation.html">conservation colouring</a>.\r
+</p>\r
+</body>\r
+</html>\r
git://source.jalview.org / jalview.git / blobdiff