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 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. +
+ +