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THANKS
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THANKS
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Over the past decades since the <tt>ViennaRNA Package</tt> first sprang to life as part
of Ivo Hofackers PhD project, several different authors contributed more and more
algorithm implementations. In 2008, Ronny Lorenz took over the extensive task to
harmonize and simplify the already existing implementations for the sake of easier
feature addition. This eventually lead to version 2.0 of the <tt>ViennaRNA Package</tt>.
Since then, he (re-)implemented a large portion of the currently existing library features,
such as the new, generalized constraints framework, RNA folding grammar domain extensions,
and the major part of the scripting language interface. Below is a list of most people
who contributed larger parts of the implementations:
- Daniel Wiegreffe (RNAturtle and RNApuzzler secondary structure layouts)
- Andreas Gruber (first approach on RNALfold Z-score filtering)
- Juraj Michalik (non-redundant Boltzmann sampling)
- Gregor Entzian (neighbor, walk)
- Mario Koestl (worked on SWIG interface and related unit testing)
- Dominik Luntzer (pertubation fold)
- Stefan Badelt (cofold evaluation, RNAdesign.pl, cofold findpath extensions)
- Stefan Hammer (parts of SWIG interface and corresponding unit tests)
- Ronny Lorenz (circfold, version 2.0, generic constraints, grammar extensions, and much more)
- Hakim Tafer (RNAplex, RNAsnoop)
- Ulrike Mueckstein (RNAup)
- Stephan Bernhart (RNAcofold, RNAplfold, unpaired probabilities, alifold, and so many more)
- Stefan Wuchty (RNAsubopt)
- Ivo Hofacker, Peter Stadler, and Christoph Flamm (almost every implementation up to version 1.8.5)
We also want to thank the following people:
- Sebastian Bonhoeffer's implementation of partition function folding served
as a precursor to our part_func.c
- Manfred Tacker hacked constrained folding into fold.c for the first time
- Martin Fekete made the first attempts at "alignment folding"
- Andrea Tanzer and Martin Raden (Mann) for not stopping to report bugs found
through comprehensive usage of our applications and RNAlib
- Thanks also to everyone else who helped testing and finding bugs, especially
Christoph Flamm, Martijn Huynen, Baerbel Krakhofer, and many more