There are a lot of different methods and a plethora of literature on this topic from a wide variety of perspectives. Here are a few highlights that might be good starting points for your search.
If your background is more musical than mathematical or computational you might be interested in the works of David Cope most of his published works focus on the analysis of classical music pieces, but he has a private venture called recombinant that seems more general. A lot of his work used music as a language type models, but I believe at least some of his most recent work has shifted more toward the whole musical genome like approach. He has a lot of software available online, but it is generally written in Lisp and some can only run in various versions of Apple's OS though some should work in Linux or anywhere you can get common lisp to run.
Analysis of signals and music in general has been a very popular problem in machine learning. There is good starting coverage in the Christopher Bishop texts Neural Networks for Pattern Recognition and Pattern Recognition and Machine Learning. Here is an example of a MSc paper that has the music classification part, but has good coverage on feature extraction, that author cites at least one of the Bishop texts and several other sources. He also recommends several sources for more current papers on the topics.
Books that are more mathematical or statistical (at least by their authorship if not by their content):
Since I mentioned Bishop and the computational perspective of machine learning I'd only be telling half the story if I didn't also suggest you take a glance at the more recent Elements of Statistical Learning (which is available for free legal download) by Hastie, Tibshirani, and Friedman. I don't remember there specifically being an audio processing example in this text, but a number of the methods covered could be adapted to this problem.
One more text worth considering is Jan Beran's Statistics in Musicology. This provides a number of statistical tools specifically for the analysis of musical works and also has numerous references.
Again there are many many other sources out there. A lot of this depends on what your background is and which approach to the problem you're most comfortable with. Hopefully at least some of this guides you a bit in your search for an answer. If you tell us more about your background, additional details about the problem, or ask a question in response to this post I'm sure I or many of the others here would be happy to direct you to more specific information. Best of luck!