The following options are available to root the tree:
The easiest method to place a root on the tree is to add an additional sequence that is 'a priori' assumed to lie outside the group of interest. Choosing option (1) or (2) then allows to select the outgroup sequence. In option (1) the root is placed such as to equalize its distance to the outgroup organism and its average distance to the remaining organisms. However, sometimes, this criterion cannot be fulfilled because the branch leading to the outgroup organism is too short. In this case, it is still possible to place the root on the latter branch, forcing the chosen organism to be the outgroup (option 2). If no 'a priori' outgroup organism is assumed (option 3), the program tries to place the root at a point where the average distance to the species on both sides is the same. It therefore scans the entire tree until such a point can be found. This sort of midpoint rooting (Swofford et al., 1996) should be chosen if an outgroup of more than one organism is used (option 3). However, in some trees, several midpoints can be found, and the program chooses the first it encounters. If you do not like the rooting point chosen by the program, the DRAW program allows rerooting of the tree at any particular internode afterwards.