Conservation Calculation

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.

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

The conservation analysis is done on each sequence group. This highlights differences and similarities in conserved residue properties between groups.