“…HMJPs, just like HMMs, do not, however, pertain to the analysis of single-photon arrival in the smFRET, 1 , 9 , 42 , 43 and, for that reason, limitations of the HMM are not intrinsic to single-photon-arrival analysis methods. However, because existing smFRET analysis, starting from single photon arrival, operates within a maximum-likelihood paradigm, it can, in principle, be reframed within a Bayesian framework, 67 such as the HMJP. Doing so, provides such methods with the ability to determine full posterior distributions, not just point estimates, around unknown quantities, thereby propagating uncertainty from the measurement into an uncertainty over the parameters of interest.…”