UNAFold

Based on the "1 error generated" and the fact that "make install" tries to do the build again, I'm guessing your build didn't succeed. :( This seems to be another error caused by the compiler treating the code as C99 instead of C89. I don't see any setting for language standard i...

OK, time for plan B. If you're up for adding a line to the source code, open src/energy.c and add this line right above the lines starting with const: void readOrDie(unsigned int num, const char* name, FILE* file, const char* format, ...); That eliminated the warnings for me, so hopefully it will el...

Hi Fabian, First, a few generalities. I don't have access to a Mac to test this myself. I know that UNAFold 4 compiles on a Mac, but I'm not sure if we ever tried UNAFold or OAA 3.8 on a Mac. (If we did, it was probably ten years ago so the results wouldn't necessarily match a modern OS/compiler any...

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 ...