X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Fcalculations%2Fconservation.html;h=9641a8e443f6ccdc57e3fbeb93c22d37edde43a2;hb=45f546c71f94606ab43389d596139606bd001656;hp=ab2310f1f7c475110ea82190fef507ee176ca33e;hpb=0696cffbccbb537be78d9fc2410589adbcd7be35;p=jalview.git
diff --git a/help/html/calculations/conservation.html b/help/html/calculations/conservation.html
index ab2310f..9641a8e 100755
--- a/help/html/calculations/conservation.html
+++ b/help/html/calculations/conservation.html
@@ -1,21 +1,24 @@
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see
Alignment Conservation Annotation
This is an automatically calculated quantitative alignment @@ -28,14 +31,21 @@ 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).
-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.