NUPACK is a growing software suite for the analysis and design of nucleic acid systems.NUPACK algorithms are formulated in terms of nucleic acid secondary structure. In most cases, pseudoknots are excluded from the structural ensemble.
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.N. Zadeh, C.D. Steenberg, J.S. Bois, B.R. Wolfe, M.B. Pierce, A.R. Khan, R.M. Dirks, N.A. Pierce.
NUPACK: analysis and design of nucleic acid systems.
J Comput Chem, 32, 170–173, 2011.