MEGA provides two options for calibrating the molecular clock for RelTime trees (where no calibration constraints have been used):
Use a single fixed time of divergence - in this case, the clock calibration is simply the (relative) height of the target node divided by fixed the time of divergence, and then this calibrated clock rate sets the scale to convert all relative times in the tree into absolute times.
Use a fixed evolutionary rate - using this option one can define a global evolutionary rate r (in units of substitutions per site per year) that is used throughout the tree. For every node in the tree whose relative height (in units of substitutions per site) is h, the divergence time of the node will be set to h/r.
Both of these options are only available from the Tree Explorer window when displaying a RelTime tree has been generated without using calibration constraints. To access this utility in the Tree Explorer window, select an internal node or a branch to focus on in the tree and click Compute | Calibrate Molecular Clock. The molecular clock dialog will then be shown and if a branch in the tree is focused, the option for using a fixed evolutionary rate will be enabled. If a node in the tree is focused, the option to use a fixed time of divergence will be enabled (in which case you can also set the scale bar title using the Time Unit edit box in this dialog).