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+
+
+
+Alignment Window Menus
+
+
+
+Alignment Window Annotations Menu (Since Jalview 2.8.2)
+
+ - Show Alignment Related
+ Show all annotations that are for the alignment as a whole (for example, Consensus,
+ or secondary structure prediction from alignment)).
+ - Hide Alignment Related
+ Hide all annotations that are for the alignment as a whole.
+ - Show Sequence Related
+ Show all annotations that are for individual sequences.
+ - Hide Sequence Related
+ Hide all annotations that are for individual sequences.
+ - Show Alignment Related
+ Show all annotations that are for the alignment as a whole (for example, Consensus).
+ - You can also selectively show or hide annotations from the Popup
+ or Annotation menus.
+ - Sort by Sequence
Sort sequence-specific annotations by sequence order in the alignment
+ (and within that, by label).
+ - Sort by Label
Sort sequence-specific annotations by label
+ (and within that, by sequence order). If neither sort order is selected, no sorting is applied,
+ allowing you to make a manual ordering of the annotations.
+ - Autocalculated Annotation
Settings
+ for the display of autocalculated annotation.
+
+ - Show first
+ Show autocalculated annotations above sequence-specific annotations.
+ Note this also applies to other annotations for the alignment, for example secondary
+ structure prediction from alignment.
+ - Show last
+ Show autocalculated / alignment annotations below sequence-specific annotations.
+ - Apply to all groups
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 Logo
Enable
+ or disable the display of the Consensus 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).
+ - Group Consensus
When
+ ticked, display a consensus row for all groups.
+
+
+
+
+
+