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The capital of Japan was Nara until in 794 Emperor Kammu moved the imperial capital from Nara to Heian-kyo, now known as the city of Kyoto.
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The Heian period that followed the Nara lasted for almost 400 years and saw the rise of the Classical period of Japanese history. The capital was in Kyoto at this point.
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A series of rebellions by the mongos followed by a civil war from 1180 to 1185, led to the victory by the Minamoto family, who then proceeded to destroy the Taira clan. The Kamakura shogunate lasted nearly 150 years and it brought political stability to Japan.
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In 1333 Samurai from the Ashikaga clan supported the emperor and the Kamakura shogunate collapsed. The Ashikaga clan turned against the emperor (Emperor Go-Daigo) and forced him to flee. From 1336, the Ashikaga clan ruled Japan as shoguns for the next 237 years. Also Christianity was introduced to Japan
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During this age of the warring states, slaves overthrew their lords, farmers led armed uprisings and the economy was seriously weakened. Japan needed a strong leader to bring peace and order back again.
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Capital moved to Edo (Tokyo) making it a stable government under the shogunate with it being isolated from the rest of the world.