Colour schemes
Jalview allows the user to set a colour scheme for the whole alignment view or for each group defined on regions within it.
To change the colour for a view, simply select a new colour scheme 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 you'll see a tick box "Apply 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 selecting a new scheme in the Colour menu.
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
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Nucleotide Colour Schemes
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