Software for the analysis of single-molecule FRET experiments
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| Confocal | OpenSMFS | A collection of tools for solution based single molecule fluorescence spectroscopy, including single-molecule FRET, FCS, MC-DEPI. |  |
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| Confocal | MFD Spectroscopy and Imaging | A software package for fluorescence spectroscopy and imaging experiments using Multiparameter Fluorescence Detection (MFD). |  |
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| Confocal | H2MM | H2MM is a maximum likelihood estimation algorithm for photon-by-photon analysis of single-molecule FRET experiments. |  |
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| Confocal | ALiX | ALiX is developed for basic research on diffusing two-color single-molecule FRET in single or multiple spot geometries. |  |
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| Confocal | Fretica | Fretica is a user-extendable toolbox for analyzing single-molecule fluorescence data in Wolfram Mathematica, with a backend written in C++. It supports both the analysis of experiments on freely diffusing and immobilized molecules. | ||
| Confocal | gSMFRETda | gSMFRETda is a C++/CUDA library for photon distribution analysis (PDA) of smFRET experiments. |  |
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| Confocal | BurstH2MM | BurstH2MM is a package for easy processing of multiparameter photon-by-photon FRETBursts data by hidden Markov Modeling (mpH2MM), that removes the need to manually recode details, and calculates of things such as E, S, transition rates, and other dwell and model parameters. BurstH2MM includes an updated/improved FRETbursts version (see OpenSMFS ) and is documented at (bursth2mm and h2mmpythonlib. H2MM was developed by Pirchi and Tuskanov et. al 2016 J. Phys. Chem. B, and extended to mpH2MM in Harris et.al 2022 Nat. Comm. BurstH2MM requires the H2MM_C package (Harris et.al), and FRETBursts (Ingargiola et. al 2016 PLoS One) to make the analysis process easier for single-molecule FRET data. | ||
| Confocal Ensemble Modelling | ChiSurf | ChiSurf is a fluorescence analysis platform for the analysis of time-resolved fluorescence decays. |  |
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| Confocal Imaging | rFRET | rFRET is a comprehensive, Matlab-based program for analyzing ratiometric microscopic FRET experiments. |  |
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| Confocal Imaging Ensemble | PAM - PIE Analysis with MATLAB | PAM is short for PIE Analysis with MATLAB – it is a GUI-based software package for the analysis of fluorescence experiments and supports a large number of analysis methods ranging from single-molecule methods to imaging. |  |
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| Modeling | LabelLib | LabelLib is a C++ library for the simulation of the accessible volume (AV) of small probes flexibly coupled to biomolecules. |  |
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| Modeling | FRETraj | gSMFRETda is a Python module for predicting FRET efficiencies and distributions based on multiple accessible-contact volumes (multi-ACV). The package features a user-friendly PyMOL plugin for FRET-assisted structural modeling and integrates with the Jupyter ecosystem. |  |
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| TIRF | MASH-FRET | MASH-FRET is a Matlab-based software package for the analysis of single-molecule FRET videos and trajectories. |  |
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| TIRF | TwoTone | A TIRF-FRET analysis package for the automatic analysis of single-molecule FRET movies. |  |
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| TIRF | ebFRET | ebFRET performs combined analysis on multiple single-molecule FRET time series to learn a set of rates and states. |  |
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| TIRF | smFRET analysis (Zhuang lab) | |||
| TIRF | vbFRET | vbFRET uses variational Bayesian inference to learn hidden Markov models from individual, single-molecule fluorescence resonance energy transfer efficiency time trajectories. |  |
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| TIRF | iSMS | iSMS is a user-interfaced software package for the visualization and analysis of wide-field, single-molecule FRET (smFRET) microscopy using immobilized molecules. |  |
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| TIRF | HaMMy | smFRET Analysis and Hidden Markov Modeling (Ha lab) | ||
| TIRF | SMACKS | SMACKS (Single Molecule Analysis of Complex Kinetic Sequences) is a maximum likelihood approach to extract kinetic rate models from noisy single molecule data. |  |
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| TIRF | SPARTAN | SPARTAN is a suite of tools, written in MATLAB, to facilitate single molecule FRET data analysis, including trace extraction from wide-field movies, trace selection with user-defined criteria, hidden Markov modeling, and data visualization. |  |
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To register your software package, please use the registration form below. For joint development, please also consider integrating your software package into the GitHub group Fluorescence Tools found at https://github.com/Fluorescence-Tools.