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. Sequence associated alignment annotation are shown with the seuqence's name appended.
  If the Per-sequence only tick box is not greyed out, then ticking it will limit the list of available annotation rows to just the labels for those that are sequence associated. Annotation rows on each sequence with the same label (e.g. T-COFFEE scores and protein disorder predictions) will then be used to colour its corresponding positions in the alignment.
  Per-sequence associated annotation colouring is currently only available in the Desktop.
- 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.
- Secondary structure annotation colouring
  By default, Jalview will employ the helix or sheet colours to shade sequences and columns by available secondary structure annotation tracks. In the case of RNA, each structure is processed to identify distinct RNA helices and rendered in the same way as the RNA Helices shading scheme. Structure based sequence shading was added in Jalview 2.8.2
- 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.