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<head><title>Conservation Calculation</title></head>\r
<body>\r
-<p><em>Conservation Colours</em></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>When the conservation option is selected the existing colour scheme is modified\r
- so that the most conserved columns in each group have the most intense colours\r
- and the least conserved are the palest.</p>\r
-<p> </p>\r
+<p><em>Colouring by Conservation</em></p>\r
+<p>This is an approach to alignment colouring based on the one used in\r
+ the AMAS method of multiple sequence alignment analysis (Livingstone\r
+ C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy \r
+ for the Hierarchical Analysis of Residue Conservation.CABIOS Vol. 9\r
+ No. 6 (745-756)). \r
+</p>\r
+<p>Conservation is measured as a numerical index reflecting the\r
+ conservation of physico-chemical properties in the alignment:\r
+ Identities score highest, and the next most conserved group contain\r
+ substitutions to amino acids lying in the same physico-chemical\r
+ class.</p>\r
+<p>For an already coloured alignment, the conservation index at each\r
+ alignment position is used to modify the shading intensity of the\r
+ colour at that position. This means that the most conserved columns\r
+ in each group have the most intense colours, and the least conserved\r
+ are the palest. The slider controls the contrast between these\r
+ extremes.</p>\r
+<p>Conservation can be calculated over the whole alignment, or just\r
+ within specific groups of sequences (such as those defined by\r
+ <a href="../calculations/tree.html">phylogenetic tree partitioning</a>).\r
+ The option 'apply to all groups' controls whether the contrast\r
+ slider value will be applied to the indices for the currently\r
+ selected group, or all groups defined over the alignment.</p>\r
</body>\r
</html>\r
git://source.jalview.org / jalview.git / blobdiff