README

#StochHMM - A Flexible hidden Markov model application and C++ library.

StochHMM is an easy to use and flexible hidden Markov model (HMM)
application and C++ library. It implements HMMs from a simple
user-defined text file. Thereby, allowing researchers to focus on the
design and optimization of the model rather than spending precious time
implementing HMM algorithms.

StochHMM implements standard HMM, HMM with duration and in the future
will implement hidden semi-Markov model architectures and algorithms. It
grants researchers the power to integrate additional datasets in their
HMM to improve predictions. Finally, it adapts HMM algorithms to provide
stochastic decoding giving researchers the ability to explore and rank
sub-optimal predictions.

We are providing StochHMM source which can be compiled and used a a 
standalone application and/or static C++ library to give researchers the
ability to rapidly develop HMMs.

StochHMM and compiles on Windows, Mac OSX, and Linux. We are providing
StochHMM under the MIT open source license to increase accessibility and
to give researchers the ability to use it in derivative works without
restrictions.  See COPYING

StochHMM is developed by Paul Lott, Korf Lab, University of California, Davis

##Additional References:

1.  Schroeder, D. I., Lott, P., Korf, I. & LaSalle, J. M. Large-scale
methylation domains mark a functional subset of neuronally expressed
genes. Genome Res 21, 1583–1591 (2011).

2.	Ginno, P. A., Lott, P. L., Christensen, H. C., Korf, I. & Chédin,
F. R-loop formation is a distinctive characteristic of unmethylated
human CpG island promoters. Mol. Cell 45, 814–825 (2012).

#For Questions, Suggestions, or Assistance, please contact Paul Lott
#(lottpaul@gmail.com)


#Installation

To compile StochHMM in Unix command-line (Linux, Mac OS X)

 $ ./configure
 $ make
Compiled application ./stochhmm will be located in the projects root folder and the static
library will be in the src/ folder.


To compile StochHMM in XCode (Mac OS X only)

1. Open the StochHMM.xcodeproj in the Xcode directory.   
2. Select the Debug/Release within the StochHMM Scheme. 
3. Select Run

Compiled target will be accessible from Xcode


#Examples
To run the examples,

$ cd bin/
$ stochhmm -model ../examples/Dice.hmm -seq ../examples/Dice.fa -viterbi -label
$ stochhmm -model ../examples/3_16Eddy.hmm -seq ../example/3_16Eddy.fa -viterbi -gff
$ stochhmm -model ../examples/3_16Eddy.hmm -seq ../example/3_17Eddy.fa -posterior
$ stochhmm -model ../examples/Dice.hmm -seq ../examples/Dice.fa -stochastic viterbi -rep 10 -label
$ stochhmm -model ../examples/Dice.hmm -seq ../examples/Dice.fa -stochastic posterior -rep 10 -label