Introduction This deposit contains the softwares used in the paper: "Spot-On: robust model-based analysis of single-particle tracking experiments". These scripts should enable a user to reproduce the full simulations and analyses performed in the paper. Some of the softwares are hosted elsewhere, and we only reference to them in this description. In this folder 170718_simSPT_simulations.zip : contains the code to generate the confined motion simulation, including a comprehensive README detailing all the parameters used for the simulation. A more updated version of the software to perform simulations (called simSPT) is available on Gitlab: https://gitlab.com/tjian-darzacq-lab/simSPT and the exact version used for the simulations is version 1.0: https://gitlab.com/tjian-darzacq-lab/simSPT/tags/v1.0 MSDi_code.zip : contains the code to analyze the simulated trajectories using a procedure derived from single-trajectory MSD fitting. This code derives from MSDanalyzer (https://tinevez.github.io/msdanalyzer/), where a fitting of the distribution of the histogram of the fitted coefficients has been added. vbSPT_comparison.zip : contains the code to analyze the simulated trajectories using the vbSPT software (http://vbspt.sourceforge.net/). Additional scripts take care of the generation of a set of instruction files that automate the analysis of the simulated dataset, and come with a comprehensive README file. Online repositories Some tools we used are not included in this folder, because they have their own, well-maintained online repositories. This is the case for Spot-On (all Matlab, web and Python versions) and simSPT, that can be accessed through the following links: https://gitlab.com/tjian-darzacq-lab/Spot-On https://gitlab.com/tjian-darzacq-lab/spot-on-matlab https://gitlab.com/tjian-darzacq-lab/Spot-On-cli About the LICENSE All the code uploaded below is Open-Source, but might have a different license than the CC-BY specified by Zenodo. This is because Zenodo does not seem to allow to specify licenses such as the GNU/GPL.