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Distorted tone, clean low end?

I use my Helix to do exactly this. It has a crossover split parameter that lets select a frequency, split it into two paths above and below and stick anything you like in each path. Work brilliantly.

Before I got the helix, I used an EBS Billy Sheehan drive pedal. This has blendable clean and drive, but crucially, it also has insert fx loops for both the clean and dirty signals. I simulated a crossover by putting an eq pedal in each loop. Actually, thinking about it, I set the clean eq to slightly scoop and the dirty eq to affect the midrange, but you get the idea.
 
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I'd probably look at the Source Audio Ultrawave. Nate Navarro did a good YouTube demo of it, it's a wildly flexible effect unit and pretty damn cheap. And it encompasses exactly what you're wanting - multiband processing.

For me, I get enough of the natural low end from my bass that I want through the Darkglass Alpha Omega - you've gotta keep in mind overdrives work by adding/boosting harmonics in the waveform, with the better drive sounds coming from an emphasis on even numbered harmonics. So really, your fundamental should stay unfettered, with boost starting to come in on the 2nd harmonics, and then hopefully emphasising the 4th, 6th, 8th etc, with special focus on the doubled frequencies, otherwise known as octaves.

One other one to consider is the Electro-Harmonix Deluxe Bass Big Muff Pi, which runs a LPF on your clean signal blend, and a HPF on your effected signal. Pretty versatile drive/distortion.
 
There’s nothing like bi-amping for this. Split your signal, run one into your fave distortion and into one amp, run the other split directly into a clean amp. I’ve been doing this for ages, and it is wonderful. Clean bottom, plus great effects
 
I stand corrected, the Broughton only creates a single external loop, meaning you can't treat the low end, only feed it in clean which may sound a little weak when compared to the more compressed high end.
This pedal is anything but weak in my experience. I use it as a light OD and it is thick with good top end presence.

One person's definition of light OD is too saturated for another.
 
I play with an overdriven tone, more of a tube growl than out and out distortion - very dynamic and suitable for soul to rock. I have recently been wonding how I might clean up just the bottom couple of octaves, day 40 to 160? I run my pedals with a parallel / mix of something like 50/50 and love my tone, but even on 50/50 the super lows can get pretty gnarly... I think I want a pedal that can separate out the frequency bands and treat them independently... Anyone had the same thoughts and found a workable and successful solution? I'm a super experienced player with a heavy gigging and studio schedule but have never come across anything in pedal form that can do what I'm asking, which is something I do in the studio all the time!

The way I do this is to do my pedal board in parallel instead of series. I split the signal 4 ways and I have 4 parallel lines of effects and I mix clean and dirty signals together and I recombine them back together. Geddy Lee and Billy Sheehan also do parallel effects. Also Chris Squire did this with Ric o Sound when he split his signal 2 ways.
 
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Since it hasn't been mentioned: the Damnation Audio Bloop would seem to do the trick, mixing in clean lows from 1K and below (you can set where the roll off happens).
True Bypass Looper & Clean Blend Pedal | Damnation Audio Bass Effects
Thanks for responding :) What this pedal doesn't do is create 2 independently treatable audio loops. This means I can distort my high end but cannot treat the low end (and a clean sub against a distorted high is likely to sound weak without compression).
 
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The way I do this is to do my pedal board in parallel instead of series. I split the signal 4 ways and I have 4 parallel lines of effects and I mix clean and dirty signals together and I recombine them back together. Geddy Lee and Billy Sheehan also do parallel effects. Also Chris Squire did this with Ric o Sound when he split his signal 2 ways.
Would love to see how you achieve this. Is your board the size of a football field? :)