Group Conservation Analysis

  1. In the View menu in the alignment window, select New View to create a new view (View 1).

  2. Ensure the annotation panel is displayed (Annotations $\Rightarrow$ Show Annotations is toggled on).

  3. Enable the display of consensus annotation rows for each group by selecting the option in the Annotation $\Rightarrow$ Autocalculated Annotation $\Rightarrow$ Group Consensus.

  4. Displaying the sequence logos makes it easier to see the different residue populations within each group. Activate the logo by right clicking the name of the Consensus annotation to open the context menu and select the Show Logo option.

  5. Alter its height, by moving the cursor onto the annotation row, right clicking the mouse and dragging it up. Rearrange the order, by right clicking the name of the Consensus annotation and dragging it up to the top of the annotations above the group annotations.

  6. Subdivide the alignment according to this selection using Select $\Rightarrow$ Make Groups for Selection.

  7. Re-order the alignment according to the new groups that have been defined by selecting Calculate $\Rightarrow$ Sort $\Rightarrow$ By Group.

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.