Constrained Hidden Markov Models in PRISM

This is an implementation of a constrained hidden Markov model in PRISM.
The particular implementation is a pair HMM which is usuable for constrained
sequence alignment. The implementation includes a few well-known global
constraints which may be used with the model.

The purpose of this implementation is to illustrate implementation principles
of constrained HMMs. 

The main file is chmm.pl which constraint the basic machinery for integration
of side-constraints into PRISM models and some basic constraint checkers.

Examples of PRISM models with side-constraints using this framework can
be found in the examples/ directory.