X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fcalculations%2Fconservation.html;h=b9d4b6f5be44ead6db69b36aa497635f606ae693;hb=b9b0c4c90f6ac88f6f5a1300d1dc4f3e83c79eb2;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/calculations/conservation.html b/help/html/calculations/conservation.html index e18e273..b9d4b6f 100755 --- a/help/html/calculations/conservation.html +++ b/help/html/calculations/conservation.html @@ -1,18 +1,52 @@ +
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.
+