HelixPSO is a multi swarm algorithm that searches the conformation
space of an RNA sequence for low lying structures. Fitness is a combination of free energy
and agreement with the centroid structure in the thermodynamic ensemble. HelixPSO has been
used on sequences of up to 1500 nucleotides.
The first version of the algorithm assesses fitness
based on thermodynamic information alone.
The extended version of the paper calculates fitness
from thermodynamic information as well as centroid information.