Subtree Menu (in Tree Explorer)

This menu contains the tree manipulation options Swap This command changes the cursor to the 'Flip' icon. Then, you click on an interior branch, MEGA swaps the two subtrees defined by this branch. If each of the subtrees is an individual taxon, then Swap is the same as Flip. The cursor will revert to the arrow if you click on the arrow icon on the left-hand side of the Tree Explorer.RH_Swap, Flip This command changes the cursor to the 'Flip' icon. Then, if you click on an interior branch, MEGA reverses the order of the lineages defined by this branch. The cursor will revert to the arrow if you click on the arrow icon on the left hand side of the Tree Explorer.RH_Flip This command changes the cursor to the 'Flip' icon. Then, if you click on an interior branch, MEGA reverses the order of the lineages defined by this branch. The cursor will revert to the arrow if you click on the arrow icon on the left hand side of the Tree Explorer. and Compress/ExpandRH_Compress_Uncompress.  In addition, by clicking on the corresponding items in the menu (for which there are tool buttons on the left), you can specify the rootRH_Rooted_tree of the tree, and display a subtree (a portion of the tree defined by a given internal branch A branch is a line connecting either two internal nodes to each other or an external node to an internal node in a phylogenetic tree. The length of a branch denotes the genetic distance (e.g., number of substitutions per unit time) between the two taxa it connects.) in a separate window. 

Many of these functionalities are also available through tools in the toolbar on the left side of the displayed tree.