X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fconsensus.html;h=7c566118fa3f4743e48a02fbe8bd7516764dc08f;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=dfb568e99328b8333299e0747f28fe28c17dbddc;hpb=c53aeee9a688f68d64106a968876e542f701fbc6;p=jalview.git
diff --git a/help/html/calculations/consensus.html b/help/html/calculations/consensus.html
index dfb568e..7c56611 100644
--- a/help/html/calculations/consensus.html
+++ b/help/html/calculations/consensus.html
@@ -1,26 +1,29 @@
+ * 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.
+ residue per column. By default this calculation includes gaps in columns.
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
@@ -30,6 +33,17 @@
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 occurring 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.
+