Yes, I'd say it takes some basic math/programming knowledge to write a FFT program. Not Master's degree since I learned how in just a university BS degree program, in fact some advanced classes in High School do such things.
In two seconds of google searching I found a windows program called cooledit
that does "Analyze audio with Spectral View and Frequency Analysis".
http://www.sonicspot.com/cooledit/cooledit.html
I've actually have used cooledit for basic frequency analysis before and it will do what you want.
Now finding a Linux program is left as an exercise for the student.