ScalaBLAST is a high-performance multiprocessor implementation of the NCBI BLAST library. ScalaBLAST supports all 5 primary program types (blastn, blastp, tblastn, tblastx, and blastx) and several output formats (pairwise, tabular, or XML). ScalaBLAST will run on most multiprocessor systems that have MPI installed, and can run over a wide variety of interconnects including infiniband, quadrics, and ethernet. ScalaBLAST is designed to run a large number of queries against either large or small databases. ScalaBLAST parallelizes the BLAST calculations by dynamically scheduling them across processors using a fault-resilient scheme.