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.