The GHMM is a freely available C library implementing efficient data structures and algorithms for basic and extended HMMs with discrete and continous emissions.
Hammock is a tool for peptide sequence clustering. It is able to cluster extremely large amounts of short peptide sequences into groups sharing sequence motifs.
VIPR is a software tool for analyzing diagnostic microarrays. The VIPR algorithm is based on a Bayesian statistical framework and requires a training set of positive control hybridizations representing the desired diagnostic targets. The advantage of a probabilistic algorithm in this context is that the positive control data can be used to improve classification of unknown infections. VIPR version 2.0 also includes functionality for detecting recombinant viruses using a hidden Markov model.
VIPR HMM is a hidden Markov model for detection recombination with microbial detection microarrays.
::DEVELOPER
Wanglab , Washington University School of Medicine
The XHMM C++ software suite was written to call copy number variation (CNV) from next-generation sequencing projects, where exome capture was used (or targeted sequencing, more generally).