vbSPT Files

 vbSPT is a program suite for analysis of single particle diffusion
 trajectories, where the diffusion constants switch randomly according
 to a discrete Markov process. The program runs on Matlab, but uses
 compiled C-code to speed up the most computer intensive loops.  The
 latest version of the software as well as a forum for discussion and
 questions can be found at 'sourceforge.net/projects/vbspt/'.

 ========================================================================= 
 Copyright (C) 2017 Martin Lindén, Fredrik Persson, and Johan Elf
 
 E-mail: 
 bmelinden@gmail.com, freddie.persson@gmail.com, johan.elf@gmail.com
 =========================================================================

 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
 the Free Software Foundation, either version 3 of the License, or any
 later version.  This program is distributed in the hope that it will
 be useful, but WITHOUT ANY WARRANTY; without even the implied
 warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See
 the GNU General Public License for more details.
 
 If you use vbSPT please cite: "Person F,Lindén M, Unoson C, Elf J,
 Extracting intracellular reaction rates from single molecule tracking
 data, Nature Methods 10, 265–269 (2013). doi:10.1038/nmeth.2367"
 
 You should have received a copy of the GNU General Public License
 along with this program. If not, see <http://www.gnu.org/licenses/>.

 This product includes software developed by Martin Lindén (in HMMcore/), 
 and by Jan-Willem van de Meent (in external/), see copyright in individual 
 files.
 =========================================================================
v 1.1.4 (bugfix, 2017-04-11):
 - changed vbSPTstart so that it can be called from any folder.
 - new function to plot model+bootstrap s.e.m: VB3_printModel.m
 - adopt displayHMMTrajs.m to current trajectory format
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v 1.1.3 (2015-12-08): 
 - VB3_getResult.m handles calls with runinput files in different folders
 - changed how parallellization in handled, to adhere to the new set
   of commands (parpool, gcp) in matlab R2015b. Users with old matlab
   versions might wish to stick with 1.1.2.
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v 1.1.2 (2014-11-19): minor bugfix, mainly to satisfy new mex compiler
 - removed C++ style comments in HMMcore*.c files to please the mex
   compiler. 
 - recompiled 64bit mex binaries for linux, mac, and windows 7
 - corrected handling of aggregation indices in VB3_removeState.m (not
   relevant for standard usage)
 - corrected typo in Eq S69 of vbSPT manual (n_j -> \tilde n_j in the
   first KL term for \gamma). Note that the code was correct all the
   time, so computational results are not affected.
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v 1.1.1 (2014-10-11): minor bugfix release
 - corrected a sign error in the KL divergence of the initial state vector 
  (the faulty terms was gammaln of the total prior weight, and so very 
   unlikely to make any practical difference).
 - corrected some internal function names to be consistent with file names.
 - made VB3_readData handle input files without the .m ending
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v 1.1 (2013-11-12): code speed-up
 - better representation of data leads to a significantly faster
   execution (~10-fold on our test data).
 - A new parameterization of the transition rates, allowing more
   flexible priors for advanced users (See manual). For non-advanced
   users, the old priors (Nat. Meth 2013 paper) are still default.
 - updated VB3_displayHMMmodel and VB3_getTrjStats to the new model format.
 - deleted VB3_reorder.m (obsolete, replaced by VB3_sortModel.m)
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 v 1.0.1 (2013-05-31): bugfix release
 - getDwellTRJ.m : consistent function name in m-file, and better handling 
   trajectories with not all states present.
 - VB3_HMManalysis.m : added functionaly to create non-existent target
   folders.
 - VBviterbi_log.c   : fixed bug in viterbi algorithm.
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