Tree Based Conservation Analysis

1. Load the PF03460 PFAM seed alignment using the sequence fetcher. Select Colour $\Rightarrow$ Taylor $\Rightarrow$ By Conservation, set Conservation shading threshold at around 20.

2. Build a Neighbour joining tree by selecting Calculate $\Rightarrow$ Tree or PCA... in the align- ment window. In the dialogue box, select Neighbour Joining and in the drop-down list select BLOSUM62, then click the Calculate button.

3. Use the cursor to select a point on the tree to partition the alignment into groups.

4. Select View $\Rightarrow$ Sort Alignment By Tree option in the tree window to re-order the sequences in the alignment. Examine the variation in colouring between different groups of sequences in the alignment window.

5. You may find it easier to browse the alignment if you first uncheck the Annotations $\Rightarrow$ Show Annotations option. Open the Overview Window from the View menu to aid navigation.

6. Try changing the colourscheme of the residues in the alignment to BLOSUM62 (whilst ensuring that Apply Colour to All Groups is selected).

Note: You may want to save the alignment and tree as a project file, since it is used in the next set of exercises.