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-<p>Conservation </p>\r
+<p><strong>Conservation Calculation</strong></p>\r
+<p>This option is based on the AMAS method of multiple sequence alignment analysis \r
+ (Livingstone C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy \r
+ for the Hierarchical Analysis of Residue Conservation.CABIOS Vol. 9 No. 6 (745-756)). \r
+ <br>\r
+ Hierarchical analysis is based on each residue having certain physico-chemical \r
+ properties. </p>\r
+<p>The alignment can first be divided into groups. This is best done by first \r
+ creating an average distance tree (Calculate->Average distance tree). Selecting \r
+ a position on the tree will cluster the sequences into groups depending on the \r
+ position selected. Each group is coloured a different colour which is used for \r
+ both the ids in the tree and alignment windows and the sequences themselves. \r
+ If a PCA window is visible a visual comparison can be made between the clustering \r
+ based on the tree and the PCA. </p>\r
+<p>The grouping by tree may not be satisfactory and the user may want to edit \r
+ the groups to put any outliers together. </p>\r
+<p>The existing colour scheme is modified so that the most conserved columns in \r
+ each group have the most intense colours and the least conserved are the palest</p>\r
+<p>The conservation analysis is done on each sequence group. This highlights differences \r
+ and similarities in conserved residue properties between groups. </p>\r
+<p></p>\r
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git://source.jalview.org / jalview.git / blobdiff