UNAFold vs. mfold

[cfgauss]

I understand there is a charge for UNAFold (through RPI) but not mfold. Is there an online list of advantages of UNAFold over mfold for DNA folding?

[nmarkham]

First, I want like to clarify that mfold and UNAFold both require licenses for commercial use. However, it does appear to be true that mfold is freely available for non-commercial use while UNAFold is not. (The "processing fee" associated with an academic license for UNAFold it not intended to be a significant obstacle, although I understand that the requirement to obtain a license in the first place may turn some people off!)

Anyway, this is a very good question. We should probably feature this information more prominently on the web site, but I'll list a few differences here for now:

1. UNAFold can handle hybridization, i.e. simulating dimers, while mfold can only simulate monomers.
2. UNAFold can compute partition functions and base pair probabilities for the entire ensemble of possible structures, while mfold focuses on minimum energy structures and selected suboptimal structures.
3. UNAFold can simulate ensembles of multiple species, while mfold can really only simulate a two-state model.
4. UNAFold runs on Windows, Linux, Mac and just about any other platform; mfold does not support Windows.
5. UNAFold uses the newest RNA energy rules from the Mathews lab, in addition to the older RNA (and DNA) rules that mfold supports.
6. UNAFold can utilize multiple CPU cores for enhanced performance over mfold.

(I'm deliberately including some important differences that don't apply to "DNA folding", for posterity!)