Depending on your use case, for a fantastic tool that lets you view spectrograms and more in realtime baudline is great: http://www.baudline.com/
For offline and very deep analysis of sounds, sonic visualizer is fantastic: https://www.sonicvisualiser.org/
And for editing sounds as component partials graphically, SPEAR is also still great: http://www.klingbeil.com/spear/
By CDP do you mean the Composers Desktop Project? I’d love to see a thread about that – would be curious to hear your experience with it. I’ve studied the source code some but still haven’t gotten around to spending much time with it admittedly even though it was recently made free: https://www.composersdesktop.com/
Also Max/MSP has plenty to offer in the frequency domain. You can patch at the lower levels with ifft and friends if I remember correctly, and the fftease externals by Eric Lyon and Chris Penrose are a great resource for a ton of useful and sometimes esoteric premade frequency domain effects.