Trees
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Following on from the principal component analysis exercise, place the cursor on the tree window to divide the tree to give about 4 groups.
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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.
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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.
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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.
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Deselect groups in the tree by moving the cursor to the far right.
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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.