The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. The NUPACK web server (http://www.nupack.org) currently enables: • Analysis: thermodynamic analysis of dilute solutions of interacting nucleic acid strands. • Design: sequence design for complexes of nucleic acid strands intended to adopt a target secondary structure at equilibrium. • Utilities: evaluation, display, and annotation of equilibrium properties of a complex of nucleic

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... id strands. NUPACK algorithms are formulated in terms of nucleic acid secondary structure. In most cases, pseudoknots are excluded from the structural ensemble.