This menu contains the tree manipulation options Swap, Flip and Compress/Expand. In addition, by clicking on the corresponding items in the menu (for which there are tool buttons on the left), you can specify the root of the tree, and display a subtree (a portion of the tree defined by a given internal branch) in a separate window.
Choosing ‘Divergence Time’ transforms the cursor to an arrow below which is the icon associated with the divergence time option. To obtain the evolutionary rate of a specific lineage, you should point the cursor to that branch and click. On the other hand, if you are interested in the average evolutionary rate of a cluster of two or more taxa, then you should click at the node at the common ancestor of the cluster. Either way, MEGA brings up the Divergence Time dialog box, which displays the evolutionary rate information for a given divergence time.
Many of these functionalities are also available through tools in the toolbar on the left side of the displayed tree.