Analysis and design of nucleic acid molecules and multistranded systems (NUPACK home page).
Simulation of kinetics for multistranded nucleic acid systems at the secondary structure level. (Link coming soon; contact schaeffer at dna.caltech.edu for a pre-release version.)
Multistrand will soon be integrated with the domain-level strand displacement programming environment developed at Microsoft Research by Luca Cardelli and Andrew Phillips (DSD)
Stochastic simulation of tile-based self-assembly (Xgrow home page).
Computer-aided design of DNA origami nanostructures, developed in William Shih's lab at Harvard (caDNAno home page). We are developing some extensions to this software that allow for insertion of single-stranded loops. (Link coming soon; contact woo at caltech.edu for more information.)
Nanoengineer is a molecular nanotechnology CAD program developed by Nanorex, Inc. (Nanrex home page). Rothemund consulted on the DNA origami and structural DNA nanotechnology features.