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: