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.
  
• Sequence ID
  Shades sequences using their Sequence ID colour. Useful when performing tree based subfamily analysis.
• 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.