Because this sort of analysis involves doing a lot of number crunching on arrays and matrices of binary integers and floats, most people opt for compiled code rather than scripting languages to do the heavy lifting.

Pick a decent compiled signal analysis library (there are at least a few open source projects with good support); it'll probably have command-line tools so that you can easily write perl wrappers for managing processing pipelines, keeping files organized, reporting results, etc.

You could also try writing perl XS code to link your scripts directly to library functions, but you might find it difficult to do better this way than you would if you were just using compiled command-line tools.