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The Wickhambrook Manuscript, a collection of English lute music compiled in the 1590s, by various composers including John Dowland. (The digitized version of this manuscript is available only to computers on the Yale network.)
The Lowell Mason Codex, a collection of 17th and 18th century organ music by various composers including Buxtehude.
The Mellon Chansonnier, a beautiful manuscript from 15th-century Naples that belongs to the Beinecke Rare Book and Manuscript Library.