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)). +
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
+ 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 +
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 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 +
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.