1. Following on from the principal component analysis exercise, place the cursor on the tree window to divide the tree to give about 4 groups.

  2. In the tree window, select View $\Rightarrow$ Sort Alignment by Tree. The sequences in the alignment are reordered to match the order in the tree and groups are formed implicitly.

  3. Place the mouse cursor on one of the first nodes in the tree and double click to invert the leaves. Select View $\Rightarrow$ Sort Alignment by Tree again and this reorders the sequences in the alignment window.

  4. Select Calculate $\Rightarrow$ Calculate Tree or PCA… in the alignment window menu. In the dialog box, select Average Distance, BLOSUM62 and click Calculate. A new tree window appears and the two tree share the same branch colouring, making it easy to compare the two trees.

  5. Deselect groups in the tree by moving the cursor to the far right.

  6. In the alignment window, click and drag the cursor to select a region from sequence 2 (column 60) to sequence 12 (column 123). (If you make an error in the selection use the [ESC] key to clear the selection.) Select Calculate $\Rightarrow$ Calculate Tree or PCA…, in the dialog box select Neighbour Joining, BLOSUM62 and Calculate. A tree will appear containing 11 sequences. Click on the tree window and divide the tree into groups. The other two trees also reflect the new group colours.

For more information on this topic go to section 6.2 of the Jalview manual.
 This exercise can be viewed in the Calculating and Displaying Trees video.