Colouring Alignment

1. Use Window $\Rightarrow$ Close All in the Jalview desktop menu to close all windows.

2. Load an alignment by selecting File $\Rightarrow$ Input Alignment $\Rightarrow$ From URL and paste in the URL https://www.jalview.org/tutorial/alignment.fa and click OK.

Note: In the Colour menu, ensure the Apply Colour To All Groups flag is not selected (not ticked).

3. Select Colour $\Rightarrow$ Clustalx in the alignment window. Try the other colour schemes in the Colour menu. Note that some colour schemes do not colour all residues.

4. Colour the alignment using Colour $\Rightarrow$ Blosum62 score. Select a group of around 4 similar sequences with some uncoloured residues by clicking and dragging. Create a group using by right-clicking on a residue in the group, in the context menu select Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour $\Rightarrow$ Blosum62 score to colour the selection. Notice how some residues which were not coloured are now coloured. The calculations performed for dynamic colouring schemes like Blosum62 are based on the selected group, not the whole alignment.

5. Colour the alignment using Colour $\Rightarrow$ Taylor, this colours the alignment except the group. Select Colour $\Rightarrow$ By Conservation.

6. In the Conservation Colour Increment dialog box, tick option Apply to all Groups and slide the selector from side to side and observe the changes in the alignment reflecting the conservation scores in the annotation row.

Note: If you don’t see any changes in appearance, it might be because sequence features are currently displayed. Feature colours can be turned off by unticking View $\Rightarrow$ Show Sequence Features option in the alignment menu.