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 Per-sequence only tick box is not greyed out, then ticking it will limit the available annotation rows to just those that are sequence associated (e.g. T-COFFEE scores and protein disorder predictions), which will colour each sequence according to its own per-residue scores.
  Per-sequence associated annotation colouring was introduced in Jalview 2.8
- 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.
  Please Note: If no colour scheme was applied previously, then the colours for lines and labels at each position in the annotation row will be used, for secondary structure symbols and graphs, this may be black by default, so your alignment will be coloured black.
- 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.
  - 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.).
    Default min and max colours were introduced in Jalview 2.7
- 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.