Colour Schemes

Jalview allows the user to set a background colour for the whole alignment - and also set the colour of defined groups within the alignment.

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 automatically ticked as default and means - the chosen colour 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.

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Clustal

Zappo

Taylor

Hydrophobicity

Helix Propensity

Strand Propensity

Turn Propensity

Buried Index

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.

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