X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fconsensus.html;h=bc42278608eaff8e36a614587d0b875c377c4820;hb=b4b901505310c3bdd1809f122abed6799c2fa664;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git
diff --git a/help/html/calculations/consensus.html b/help/html/calculations/consensus.html
index e18e273..bc42278 100644
--- a/help/html/calculations/consensus.html
+++ b/help/html/calculations/consensus.html
@@ -1,18 +1,49 @@
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+Alignment Consensus Annotation
+
+Alignment Consensus Annotation
+The consensus displayed below the alignment is the percentage of the modal
+ residue per column. By default this calculation takes includes gaps in column.
+ You can choose to ignore gaps in the calculation by right clicking on the label
+ "Consensus" to the left of the consensus bar chart.
+
If the modal value is shared by more than 1 residue, a "+" symbol
+ is used in the display for the simple reason that it is not possible to display
+ multiple characters in a single character space.
+
Copying the consensus sequence
+Select the "Copy Consensus Sequence" entry from
+the consensus annotation label to copy the alignment's consensus sequence to the
+clipboard.
+
+
Sequence logo
+ By clicking on the label you can also activate the sequence logo. It
+ indicates the relative amount of residues per column which can be
+ estimated by its size in the logo. The tooltip of a column gives the
+ exact numbers for all occuring residues.
+
If columns of the alignment are very diverse, then it can
+ sometimes be difficult to see the sequence logo - in this case, right
+ click on the annotation row label and select
+ Normalise Consensus Logo to scale all columns of the
+ logo to the same height.
+
+
+