Phylogeny | Construct/Test Neighbor-Joining Tree
Or
Phylogeny | Construct/Test Minimum-Evolution Tree
A t-test, which is computed using the bootstrap procedure, is constructed based on the interior branch length and its standard error and is available only for the NJ and Minimum Evolution trees. MEGA shows the confidence probability in the Tree Explorer; if this value is greater than 95% for a given branch, then the inferred length for that branch is considered significantly positive. Select test of phylogeny for either of these trees in the Analysis Preferences dialog.
See Nei and Kumar (2000) (chapter 9) for further details.