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.