X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fconservation.html;h=d38924abd4ca6a2cc732cc318f25b16c04463828;hb=9493ac8f3b6a02d3cf9747ed6c0d6cf407d284e8;hp=7c5953f5337556fa5209b811bcf78bec1e8c27e2;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git diff --git a/help/html/calculations/conservation.html b/help/html/calculations/conservation.html index 7c5953f..d38924a 100755 --- a/help/html/calculations/conservation.html +++ b/help/html/calculations/conservation.html @@ -1,21 +1,24 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> Alignment Conservation Annotation

Alignment Conservation Annotation

This is an automatically calculated quantitative alignment @@ -28,14 +31,21 @@ is based on the one used in for the Hierarchical Analysis of Residue Conservation.CABIOS Vol. 9 No. 6 (745-756)). +View an HTML version of the paper

Conservation is measured as a numerical index reflecting the conservation of physico-chemical properties in the alignment: Identities score highest, and the next most conserved group contain substitutions to amino acids lying in the same physico-chemical class.

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Conservation is visualised on the alignment or a sequence group + as a histogram giving the score for each column. Conserved columns are + indicated by '*' (score of 11 with default amino acid property + grouping), and columns with mutations where all properties are + conserved are marked with a '+' (score of 10, indicating all + properties are conserved).

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Colouring an alignment by conservation
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Colouring an alignment by conservation
Conservation scores can be used to colour an alignment. This is explained further in the help page for conservation colouring.