Colouring by Conservation
+This is an approach to alignment colouring which highlights + regions of an alignment where physicochemical properties are + conserved. It is based on the one used in + the AMAS method of multiple sequence alignment analysis (Livingstone + C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy + for the Hierarchical Analysis of Residue Conservation.CABIOS Vol. 9 + No. 6 (745-756)). See the conservation calculation help page for + a more thorough explanation of the calculation. +
+For an already coloured alignment, the conservation index at each + alignment position is used to modify the shading intensity of the + colour at that position. This means that the most conserved columns + in each group have the most intense colours, and the least conserved + are the palest. The slider controls the contrast between these + extremes.
+Conservation can be calculated over all sequences in an alignment, or just + within specific groups (such as those defined by + phylogenetic tree partitioning). + The option 'apply to all groups' controls whether the contrast + slider value will be applied to the indices for the currently + selected group, or all groups defined over the alignment.
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