<html>\r
+<head><title>Conservation Calculation</title></head>\r
<body>\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
+<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
+ 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
+<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
+<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
+<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
+<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
</body>\r
git://source.jalview.org / jalview.git / blobdiff