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.