X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fcalculations%2Fconservation.html;h=bd4a625aec7b80e3a14976c417543515e7604be8;hb=a86681109f3b9be838ae3fb2dd9d6db544be4bce;hp=9c8f0c5af51b440cbf54599f163c0fb5df5b84a4;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git diff --git a/help/html/calculations/conservation.html b/help/html/calculations/conservation.html index 9c8f0c5..bd4a625 100755 --- a/help/html/calculations/conservation.html +++ b/help/html/calculations/conservation.html @@ -1,7 +1,7 @@ +--> Alignment Conservation Annotation

Alignment Conservation Annotation

This is an automatically calculated quantitative alignment @@ -28,14 +28,21 @@ 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.