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This excellent site provides a thorough and informed exploration of the origins of the song and its multiple renditions.
The Library of Congress has posted a page on “Yankee Doodle” as part of its Lyrical Legacy project. Here you can find lyrics, audio files, and a brief background to the song.
This site, part of the E Pluribus Unum Project, takes a short look at “Yankee Doodle” and its place in American culture over the centuries.