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