+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head><title>Alignment Consensus Annotation</title></head>
+<body>
+<p><strong>Alignment Consensus Annotation</strong></p>
+<p>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.
+<p>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.
+<p><strong>Copying the consensus sequence</strong></p>
+<p>Select the <strong>"Copy Consensus Sequence"</strong> entry from
+the consensus annotation label to copy the alignment's consensus sequence to the
+clipboard.
+
+<p><strong>Sequence logo</strong></p>
+ 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.
+ <br />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
+ <strong>Normalise Consensus Logo</strong> to scale all columns of the
+ logo to the same height.
+ </p>
+</body>
+</html>