Conservation Colours
-This option is based on 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)).
-
- Hierarchical analysis is based on each residue having certain physico-chemical
- properties.
The alignment can first be divided into groups. This is best done by first - creating an average distance tree (Calculate->Average distance tree). Selecting - a position on the tree will cluster the sequences into groups depending on the - position selected. Each group is coloured a different colour which is used for - both the ids in the tree and alignment windows and the sequences themselves. - If a PCA window is visible a visual comparison can be made between the clustering - based on the tree and the PCA.
-The grouping by tree may not be satisfactory and the user may want to edit - the groups to put any outliers together.
-When the conservation option is selected the existing colour scheme is modified - so that the most conserved columns in each group have the most intense colours - and the least conserved are the palest.
-+
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.