From: jprocter Date: Tue, 1 Mar 2005 16:51:50 +0000 (+0000) Subject: Obsolete. Explanation within the conservation colourscheme entry. X-Git-Tag: Release_2_0~629 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b40bd354721dc7103a14057504e8d917e9dc070d;p=jalview.git Obsolete. Explanation within the conservation colourscheme entry. --- diff --git a/help/html/calculations/conservation.html b/help/html/calculations/conservation.html deleted file mode 100755 index 24ba193..0000000 --- a/help/html/calculations/conservation.html +++ /dev/null @@ -1,26 +0,0 @@ - -Conservation Calculation - -

Conservation Calculation

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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.

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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.

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The grouping by tree may not be satisfactory and the user may want to edit - the groups to put any outliers together.

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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

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

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