RNA secondary structure following "Fast Folding and Comparison of RNA Secondary Structures, Hofacker et al., 1994". Uses the Turner 2004 parameter set. The algorithm work on an algebraic ring structure that is instanciated as required. This prelimenary release contains the minimum-free energy version only.
Do not expect good runtimes with anything less than 6.13.201008xx. The newest head produces an executable roughly 20x faster than GHC 6.12.3.
Bugs are likely present in this algorithm. If you find one, please send me a mail.
One goal is to get the vector library to optimise the loops (fold's) in such a way as to get performance close to the ViennaRNA package. Right now, we are about 15x slower.
Works well with -Odph, -fllvm (llvm is about 70% faster than
0.0.0.3 forgot a lot of depends!