X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fconservation.html;h=4cfc825e811f6877686d43f4d2241b8b49c84fff;hb=eea2b610bea04896964d403093df1141a16efd5f;hp=8c17f68f9c160056f910495ff23b69505480229b;hpb=6fa9683bef52d6709abb81840681e4fa452cafe7;p=jalview.git diff --git a/help/html/calculations/conservation.html b/help/html/calculations/conservation.html index 8c17f68..4cfc825 100755 --- a/help/html/calculations/conservation.html +++ b/help/html/calculations/conservation.html @@ -1,5 +1,27 @@ - -

Conservation

+Alignment Conservation Annotation +

Alignment Conservation Annotation

+

This is an automatically calculated quantitative alignment +annotation which measures the number of conserved physico-chemical +properties conserved for each column of the alignment. Its calculation +is based on the one used in + the AMAS method of multiple sequence alignment analysis :
+

+

+

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.

+ +

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. +