The work described herein was performed using the Sequence Alignment and Modeling (SAM) HMM software suite (http://www.cse.ucsc.edu/research/compbio/sam.html). Code development and performance analysis was performed on a DEC Alpha 255 with a 233MHz clock, 96MBytes of main memory, and a 1Mbyte external cache. SAM is written in ANSI C and was compiled using the Alpha's native compiler at its highest optimization level.