X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Falwview.html;h=53ae079702193aaf7cf8a4bc1d1d569a02d0d10c;hb=524f1bc53749f18e8217ec14b72d3a2a444c072f;hp=85ffe3639faf8b26ee894be88c6e69b7da451df4;hpb=aff93619ba53584f9b01970832558331951d9dbf;p=jalview.git
diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html
index 85ffe36..53ae079 100755
--- a/help/html/menus/alwview.html
+++ b/help/html/menus/alwview.html
@@ -1,4 +1,21 @@
+
Alignment Window Menus
@@ -25,17 +42,22 @@
Autocalculated Annotation
Settings for the display of autocalculated annotation.
-
Apply to all groups
- When ticked, any settings will be applied to all autocalculated annotation.
+ When ticked, any modification to the current settings will be applied to all autocalculated annotation.
-
Show Consensus Histogram
Enable or disable the display of the histogram above the consensus sequence.
-
- Show Consensus Profile
+ Show Consensus Logo
Enable or disable the display of the sequence logo above the consensus sequence.
- -
+
- Normalise Consensus Logo
+ When enabled, scales all logo stacks to the same height,
+ making it easier to compare symbol diversity in highly variable
+ regions.
+
+ -
Group Conservation
When ticked, display a conservation row for all groups (only available for protein alignments).