Jalview allows the user to set a background colour for the whole alignment view or for each group defined on regions within it.
To change the background colour, simply select the colour from the "Colour" menu.
To change the colour of a group, right click on any residue within a group and use the popup menu to define the group colour.
At the top of the "Colour" menu the tick box "Apply Background Colour to all groups". This is ticked by default so that a chosen colour scheme will be applied to all existing groups. If you wish to maintain the colour scheme for defined groups, make sure you deselect this option before changing the background colour.
The "Colour→Colour Text..." entry opens a dialog box to set a different text colour for light and dark background, and the intensity threshold for transition between them.
The default colour schemes are summarised in the table below:
Protein Colour Schemes
Nucleotide Colour Schemes