<html>\r
-<head><title>Conservation Calculation</title></head>\r
+<head><title>Colouring by Conservation</title></head>\r
<body>\r
<p><em>Colouring by Conservation</em></p>\r
-<p>This is an approach to alignment colouring based on the one used in\r
+<p>This is an approach to alignment colouring which highlights\r
+ regions of an alignment where physicochemical properties are\r
+ conserved. It is 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
+ No. 6 (745-756)). See the <a href="../calculations/conservation.html">conservation calculation</a> help page for\r
+ a more thorough explanation of the calculation.\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
+<p>Conservation can be calculated over all sequences in an alignment, or just\r
+ within specific groups (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
git://source.jalview.org / jalview.git / blobdiff