There are two different types of methods for testing the reliability of an obtained tree. One is to test the topological difference between the tree and its closely related tree by using a certain quantity, for example, the sum of all branch lengths in the minimum evolution method. This type of test examines the reliability of every interior branch of the tree, and is generally a conservative test as compared to other tests included in MEGA.
The other type of test examines the reliability of each interior branch whether or not it is significantly different from 0. If a particular interior branch is not significantly different from 0, we cannot exclude the possibility of a trifurcation of the associated branches or that the other types of bifurcating trees can be generated by changing the splitting order of the three branches involved. Therefore, in MEGA we implement the bootstrap procedure for estimating the standard error of the interior branch and test the deviation of the branch length from 0 (Dopazo 1994).
The third type of test is the bootstrap test, in which the reliability of a given branch pattern is ascertained by examining the frequency of its occurrence in a large number of trees, each based on the resampled dataset.
Details of these procedures are given in Nei and Kumar (2000, chapter 9).