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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.
+
+
+
+