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I have about 3000 melody files encoded as MusicXML here (soon to be much more) and I'd like to be able to find a tool that will allow me to compare those melodies to each other looking for possible matches / similarities. What existing tools or algorithms are there? I can pretty easily convert these files to other formats as needed.
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Take a look at the next issue of the Journal of Mathematics and Music, which is a special issue with a lot of papers on pattern finding in music, coming out soon. A number of the papers are already published online.