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#StochHMM ##A flexible Hidden Markov Model Framework in C++

News: Check out how Matthew Porter used StochHMM to plug in custom functions to state emissions in order to quickly create a HMM to annotate copy number from SAM files. Ploidamatic Manuscript submitted for review at Oxford Bioinformatics.

1. Introduction

2. NEW Comparison to Mamot / R-HMM / HMMoc

3. Installing/Compiling StochHMM

4. Running StochHMM

   1. Running Examples

5. Developing a HMM using StochHMM

6. File Formats

   1. Model File
      1. Model Information
      2. Track Symbol Definitions
         1. Track Functions
      3. Ambiguous Symbol Definitions
      4. Scaling Values
      5. Templated States
      6. State Definitions
         1. Transitions
         2. Emissions
         3. Additional User-defined State Functions
            1. Pre-defined Univariate and Multivariate PDF Functions
   2. Sequence Files
      1. External Definitions
   3. Models Files

7. Examples Model and Sequences

   1. Simple CpG
   2. CpG with Ambiguous
   3. Simple Dice
   4. User-Defined Emissions Dishonest Casino
   5. Multiple Independent Emissions
   6. Multiple Joint Emissions

8. C++ Library

   1. Example Code
   2. Import sequence from String
   3. StochHMM main explained

9. Additional Resources