Colouring by Secondary Structure Consensus

This approach to alignment colouring highlights regions of an alignment where protein secondary structure is conserved or diverges, in the same way as with Colour by Conservation.

For an already coloured alignment, the secondary structure consensus score at each alignment position is used to modify the shading intensity of the colour at that position. This means that regions with the most conserved secondary structure in each group have the most intense colours, and the least conserved are the palest. The slider controls the contrast between these extremes.

Secondary structure consensus can be calculated over all sequences in an alignment, or just within specific groups (such as those defined by partitioning a secondary structure annotation tree ). 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.