Software

vbFRET

vbFRET uses variational Bayesian inference to learn hidden Markov models from individual, single-molecule fluorescence resonance energy transfer efficiency (EFRET) versus time trajectories as described in Bronson et al (2009) and Bronson et al (2010). The software is implemented in MATLAB and can be downloaded here.

ebFRET

ebFRET uses empirical Bayesian inference to learn a single, consensus hidden Markov model from a large population of single-molecule fluorescence resonance energy transfer efficiency (EFRET) versus time trajectories as described in van de Meent et al (2013) and van de Meent et al (2014). The software is implemented in MATLAB and can be downloaded here.

Single Molecule Dataset (SMD)

The single molecule dataset (SMD) format has been jointly developed in the groups of Dan Herschlag (Stanford) and Ruben Gonzalez to facilitate publication and exchange of data and analysis results obtained in single-molecule studies. This repository contains Matlab utility functions for creating, validating, saving and loading SMD structures in Matlab.