X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fcalculations%2Fconservation.html;h=d38924abd4ca6a2cc732cc318f25b16c04463828;hb=81edd609f9841a84d5799d221277d45413a177cf;hp=4cfc825e811f6877686d43f4d2241b8b49c84fff;hpb=8c0737632c158907098990b81ac702710721e9f2;p=jalview.git diff --git a/help/html/calculations/conservation.html b/help/html/calculations/conservation.html index 4cfc825..d38924a 100755 --- a/help/html/calculations/conservation.html +++ b/help/html/calculations/conservation.html @@ -1,27 +1,54 @@ - -
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.
-
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.
+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).
+ +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.
+