Use when computing suboptimal RNA secondary structures within an energy range above the minimum free energy, or when sampling structures from the Boltzmann ensemble.
RNAsubopt/home/vimalinx/miniforge3/envs/bio/bin/RNAsuboptreferences/help.md for complete options and parameter detailsRNAsubopt when you need a set of plausible secondary structures instead of a single best fold.-e to enumerate all structures within an energy band above the MFE for short or moderate-length RNAs.-p when exhaustive enumeration would explode and you instead want Boltzmann-weighted sampling from the ensemble.-z, -D, -c, or -g when the question is specifically about Zuker suboptimals, density of states, circular RNAs, or G-quadruplex-aware folding.--shape--sp-data# Enumerate structures within 2 kcal/mol of the MFE
printf 'GGGAAAUCC\n' | RNAsubopt -e 2
# Sample 100 structures from the Boltzmann ensemble
printf 'GGGAAAUCC\n' | RNAsubopt -p 100
# Sort enumerated suboptimal structures
printf 'GGGAAAUCC\n' | RNAsubopt -e 2 -s
# Compute density of states instead of explicit structures
printf 'GGGAAAUCC\n' | RNAsubopt -D
-i-e), stochastic sampling (-p), or Zuker suboptimals (-z)RNAsubopt with appropriate parameters (e.g., -e 3.0 for structures within 3 kcal/mol of MFE, -p 1000 for 1000 sampled structures)-e values or switch to sampling (-p) for long sequences-T for non-physiological or organism-specific conditions--noconv to preserve input exactly