NUPACK User Guide 3.0

• Overview
  • Directories
  • Compilation
  • Example job files
  • Notation and terminology
  • Secondary structure model
  • Conventions
  • License
• Executables
  • pfunc: calculate the partition function
  • pairs: calculate base-pairing observables
  • mfe: find the minimum free energy (MFE) secondary structure(s)
  • subopt: find all secondary structures within a specified free energy gap of the MFE
  • count: count the number of secondary structures in the ensemble
  • energy: calculate the free energy of a secondary structure
  • prob: calculate the equilibrium probability of a secondary structure
  • defect: calculate the ensemble defect
  • complexes: calculate the partition functions of all strand complexes up to a specified size
  • concentrations: calculate the equilibrium concentration of each complex in a dilute solution
  • distributions: calculate the equilibrium population distribution and expected value for a few complexes in a dilute solution
  • design: design the sequence of one or more strands intended to adopt a target secondary structure at equilibrium
• References