Minamoto is the man who domained Japan then. At that time, the relationship between the master and Samurai was based on Goon and Houkou. Goon means the obligation. Houkou does the service. If Samurai serve, master gives the new territory to him in return.
Second stage is between fourteenth and sixteenth century.
In those days, that relationship collapsed and many masters were killed by their subordinate. It led to many conflicts in many places in Japan. So Anybody could become the master if only he had power. Tokugawa is the name of the man who became the master in second stage and dominated Japan. That is to say ,he is the master of masters.