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Best route and way to get from Budapest to Prague via Vienna

In June, we are taking a Viking Cruise, ending in Budapest, and would like to visit Vienna and Prague before returning to Portland, OR. Do you advise stopping in Vienna first and flying out of Prague or reversing those stops? What is the best way to travel from Budapest? Train?

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Go by train from Budapest to Vienna, then by train from Vienna to Prague. Fly back home from Prague.