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

1. Introduction

2. Features

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
   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. Dice with PDF

8. C++ Library

   1. [Example Code]

9. Additional Resources