Specification and simulation of multicellular genetic programs in E. coli and yeast, developed in Eric Klavins' lab at UW (gro home page).
Analysis and design of nucleic acid molecules and multistranded systems, developed in Niles Pierce's lab at Caltech (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, developed in Erik Winfree's lab at Caltech (Xgrow home page).
Computer-aided design of DNA origami nanostructures, developed in William Shih's lab at Harvard and Shawn Douglas' lab at UCSF (caDNAno home page).
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.