UNAFold

Hi Jan, I'm sorry I didn't respond to this sooner! Unfortunately, it isn't as simple as a download link. As the page you mentioned says: Both commercial and non-commercial use require a license from RPI. See https://ipo.rpi.edu/invention/unafold-version-40 for details. (I need to update some of the ...

OK, I compared the two sequences myself (grr, six hour limit!) and I think I see the issue. For the first one, the default values for P, W and MAX mean mfold computes multiple structures — a minimum free energy structure and a sample of other, suboptimal structures. For the second, there are no subo...

I believe your interpretation is correct — depending on the settings and the sequence, it's entirely possible that mfold would consider there to be no valid structures. (UNAFold is very similar, although not necessarily identical.) If you include a link to results I can probably confirm that that's ...