Multistrand is a software package for simulating the kinetics of multiple interacting nucleic acid strands. It is developed at the Winfree lab at the California Institute of Technology.DNA and Natural Algorithms Group @ Caltech
The KinDA project bundles Multistrand along with other useful software into a Public AWS Image. Using that predefined machine image in the Amazon cloud ensures you can get started with Multistrand right away, with all of the necessary dependencies already installed.
For longer simulations and better integration with your analysis pipeline, Multistrand can also be installed locally on your system.
Detailed installation instructions can be found in the README file.