Remove Redundant Sequences

  1. Using the alignment generated in the previous exercise. In the alignment window, you may need to deselect groups using [ESC] key.

  2. In the Edit menu select Remove Redundancy to open the Redundancy threshold selection dialog box. Adjust the redundancy threshold value, start at 50 and increase the value to 62. Sequences selected will change colour in the Sequence ID panel. Select Remove to remove the sequences that are more than 62% similar under this alignment.

  3. From the tree window, select View $\Rightarrow$ Mark Unlinked Leaves option, and note that the removed sequences are now prefixed with a * in the tree view.

  4. Use the Undo button in the Redundancy threshold selection dialog box to recover the sequences. Note that the * symbols disappear from the tree display. (Alternatively, use Undo button in the Edit menu in alignment window).

  5. Experiment with the redundancy removal and observe the relationship between the percentage identity threshold and the pattern of unlinked nodes in the tree display.

For more information on this topic go to section 6.2 of the Jalview manual.