Principal Component Analysis

  1. Close all windows (Window $\Rightarrow$ Close All).

  2. Load the alignment at

  3. Select the alignment window menu option Calculate $\Rightarrow$ Calculate Tree or PCA… . A dialog box will open, select the Principal Component Analysis option and click Calculate.

  4. Move the PCA viewer window away from the alignment window. In the PCA window, rotating the plot by clicking and dragging the mouse. Clicking on points in the plot will highlight the sequences on the alignment.

  5. Deselect sequences from the alignment window using the [ESC] key. Select Calculate $\Rightarrow$ Calculate Tree or PCA … from the alignment window menu. In dialog box select Neighbour Joining, in the drop-down list select BLOSUM62 and click Calculate.

  6. Tree window opens, place the mouse cursor on the tree and a cursor will appear as a red vertical line. The line partitions the tree into a number of groups, each with a different (arbitrarily selected) colour. Place the mouse cursor on node of the branch and tooltip opens. Its colour can be changed by right clicking the mouse and selecting a different colour in the Colour dialog box.

  7. Note the colour of the sequence ID label matches both the colour of the branches in the partitioned tree and the points in the PCA plot.

For more information on this topic go to section 6.1 of the Jalview manual.