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The Gempei war was between the two great clans: The Taira clan, and the Minamoto clan. They fought a five year war for the political power of Japan. This is where the story of Yoshitsune originates from.
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During these times the Samurai held all of the political power in Japan. They were prized as the best of the fighters in all of Japan.
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The Kamakura Shogunate was the first of several centuries of a military based government.
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The Ashikaga Shogunate was another branch of the Minamoto clan that seized control after the Kamakura Shogunate was overthrown. Under this rule Japan splintered into over 400 different independent states in 1500.
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The Tokugawa Shogunate was the last Shogunate in Japanese history. During the Tokugawa reign the Samurai were disbanded. The political power of the Samurai was eliminated in 1692, so they moved on to become either scholars, monks, or simple business owners.
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The Samurai were simply hired swords for Feudal lords during this time period. They were skilled fighters and preferred by these daimyo.