<html>\r
-<head><title>Conservation Calculation</title></head>\r
-<body>\r
-<p><strong>Conservation Calculation</strong></p>\r
-<p>This option is based on the AMAS method of multiple sequence alignment analysis\r
- (Livingstone C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy\r
- for the Hierarchical Analysis of Residue Conservation.CABIOS Vol. 9 No. 6 (745-756)).\r
- <br>\r
- Hierarchical analysis is based on each residue having certain physico-chemical\r
- properties. </p>\r
-<p>The alignment can first be divided into groups. This is best done by first\r
- creating an average distance tree (Calculate->Average distance tree). Selecting\r
- a position on the tree will cluster the sequences into groups depending on the\r
- position selected. Each group is coloured a different colour which is used for\r
- both the ids in the tree and alignment windows and the sequences themselves.\r
- If a PCA window is visible a visual comparison can be made between the clustering\r
- based on the tree and the PCA. </p>\r
-<p>The grouping by tree may not be satisfactory and the user may want to edit\r
- the groups to put any outliers together. </p>\r
-<p>The existing colour scheme is modified so that the most conserved columns in\r
- each group have the most intense colours and the least conserved are the palest</p>\r
-<p>The conservation analysis is done on each sequence group. This highlights differences\r
- and similarities in conserved residue properties between groups. </p>\r
-<p></p>\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