+ 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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