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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