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.
Dynamic colour schemes
Alignments and groups may be coloured according to associated sequence and alignment annotation. Any applied colour schemes (such as those shown in the table below) can also be shaded by amino acid physico-chemical property conservation to reveal patterns of variation, or applied selectively to Above Identity Threshold.
Alignments and groups can also be shaded according to percentage abundance of aligned residues (using Percentage Identity), and for protein alignments, the BLOSUM 62 Score and ClustalX shading schemes highlight amino acid conservation.
The Sequence ID colour scheme shades sequences with the same colour assigned to their Sequence ID. Colours are assigned when groups are created by partitioning a tree or subdividing the alignment by sequence with Select→Make Groups For Selection.
Amino acid and Nucleotide based colour schemes
The built-in colour schemes based on amino acid and nucleotide symbols are summarised in the table below:
Protein Colour Schemes
Nucleotide Colour Schemes