Colouring by Conservation

This is an approach to alignment colouring 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)).

Conservation is measured as a numerical index reflecting the conservation of physico-chemical properties in the alignment: Identities score highest, and the next most conserved group contain substitutions to amino acids lying in the same physico-chemical class.

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 the whole alignment, or just within specific groups of sequences (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.