Now after I post this, I see there has been a brief discussion of analysis of competing hypotheses before on LessWrong, from which you can find an open source software for the methodology (GitHub).

I also see there are other softwares for this methodology, but none of these seem quite like what I want. I'll have to look closer.

Any other systems would be of interest to me. This is a good system for comparing competing hypotheses, but does nothing for the management of non-competing hypotheses (which could still be related).