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.