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On a few occasions I've seen some papers that apply bioinformatics dotplots (aka recurrence plots) to general files, to demonstrate things like beat detection in music, or relationships between .dll versions. I'd like to use it to identify strongly conserved portions of an audio stream are between two files.

Is there an open source program that takes two files A and B and generates a dotplot visualization of them? Or even better, one that takes two compressed audio files? I can find plenty of genetics related tools, but I'm looking for either a more generalized tool, or one specialized for audio / video.

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If you plan to be doing this a lot, you may consider making the investment in learning how to use Octave and gnuplot. I would not consider either of these beginner tools.

Interestingly, the book Audio Anecdotes has a section explaining how to use these tools to analyze audio files.

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