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-
-
-
-Alignment Window Menus
-
-
-
-
- Alignment Window Colour Menu
-
-
- - Apply Colour To All Groups
- If this is selected, any changes made to the background
- colour will be applied to all currently defined groups.
-
- - Colour
- Text ...
Opens the Colour Text dialog box to
- set a different text colour for light and dark background, and
- the intensity threshold for transition between them.
- - Colour Scheme options: None, ClustalX,
- Blosum62 Score, Percentage Identity, Zappo, Taylor,
- Hydrophobicity, Helix Propensity, Strand Propensity, Turn
- Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User
- Defined
- See colours for
- a description of all colour schemes.
-
-
- - By Conservation
- See Colouring
- by Conservation.
-
- - Modify Conservation Threshold
- Use this to display the conservation threshold slider
- window. Useful if the window has been closed, or if the 'by
- conservation' option appears to be doing nothing!
- - Above Identity Threshold
- See Above
- Percentage Identity.
-
- - Modify Identity Threshold
- Use this to set the threshold value for colouring above
- Identity. Useful if the window has been closed.
-
- - By Annotation
Colours
- the alignment on a per-column value from a specified annotation.
- See Annotation
- Colouring.
-
- - By RNA Helices
Colours
- the helices of an RNA alignment loaded from a Stockholm file.
- See RNA
- Helices Colouring.
-
-
-
-