Dynamic programming is used in bioinformatics to find good ways of labeling sequences of amino-acids or nucleotides, given that you have some model of how things can change over time. The org.biojava.bio.dp package provides a toolkit for building arbitrary HMMs that define grammers over ResidueLists. This gives you great flexibility to design your HMM on a whim, and see if it works. The down-side of this is that we can't guarantee that the performance of all algorithms will rival that of hand-edited C-code.

The demonstration applications here are to show you the sorts of things that can be done with very little effort. They are not meant as fully fledged applications, although you may choose to build an application from them.