X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fconservation.html;h=ac00ec40edd8ff7538fa0ec2830a177253b8efc8;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=904c323695a8dad65d43c19ca9873307fb206a47;hpb=c53aeee9a688f68d64106a968876e542f701fbc6;p=jalview.git diff --git a/help/html/calculations/conservation.html b/help/html/calculations/conservation.html index 904c323..ac00ec4 100755 --- a/help/html/calculations/conservation.html +++ b/help/html/calculations/conservation.html @@ -1,20 +1,21 @@ Alignment Conservation Annotation

Alignment Conservation Annotation

@@ -28,14 +29,21 @@ 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.

+

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
+

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.