Richard Hughey's research group focuses on two areas: the Kestrel programmable sequence analysis accelerator and the SAM Hidden Markov Modeling system. Kestrel is a single-board parallel processor designed to speed biological sequence analysis. The Kestrel research group, which includes Professor Kevin Karplus, designed and built the system, and has applied the machine to Smith & Waterman searching, SAM HMMs, conformational chemistry, graph coloring, and other areas. Hughey and Dr. Anders Krogh originally developed SAM – a collection of algorithms and software used to create statistical models of RNA, DNA, and protein families with profile hidden Markov models. Since then, the Hughey and Karplus groups have collaborated to extend and improve SAM.