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22 <head><title>Colouring by Conservation</title></head>
24 <p><strong>Colouring by Conservation</strong></p>
25 <p>This is an approach to alignment colouring which highlights
26 regions of an alignment where physicochemical properties are
27 conserved. It is based on the one used in
28 the AMAS method of multiple sequence alignment analysis (Livingstone
29 C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy
30 for the Hierarchical Analysis of Residue Conservation.CABIOS Vol. 9
31 No. 6 (745-756)). See the <a href="../calculations/conservation.html">conservation calculation</a> help page for
32 a more thorough explanation of the calculation.
34 <p>For an already coloured alignment, the conservation index at each
35 alignment position is used to modify the shading intensity of the
36 colour at that position. This means that the most conserved columns
37 in each group have the most intense colours, and the least conserved
38 are the palest. The slider controls the contrast between these
40 <p>Conservation can be calculated over all sequences in an alignment, or just
41 within specific groups (such as those defined by
42 <a href="../calculations/tree.html">phylogenetic tree partitioning</a>).
43 The option 'apply to all groups' controls whether the contrast
44 slider value will be applied to the indices for the currently
45 selected group, or all groups defined over the alignment.</p>