Annotation Colouring

Jalview allows the columns of an alignment to be coloured using any numerical annotation rows added to that alignment.

Select "Colour" → ".. by Annotation" to bring up the Colour by Annotation settings window.

- Select which annotation to base the colouring scheme on using the top left selection box.
- If the "Use Original Colours" box is selected, the colouring scheme will use the colouring scheme present on the alignment before the Annotation Colour Settings window was displayed.
- The colour scheme can display a colour gradient from a colour representing the minimum value in the selected annotation to a colour representing the maximum value in the selected annotation. Use the "Min Colour" and "Max Colour" to set the colour gradient range.
  - New in Jalview 2.7: Press the "Defaults" button to reset the minimum and maximum colours to their default settings (these are configured in the applet's parameters or the application's user preferences.)
- Select whether to colour the alignment above or below an adjustable threshold with the selection box center left of the window.
- Change the threshold value with the slider, or enter the exact value in the text box.
- Select the "Threshold is Min/Max" checkbox to assign colours using the thresholded range's minimum and maximum values, otherwise the scale will be defined by the range of values in the annotation row.