SPS SWAT, SPS Cross_Match, and SPS Phrap are based on Phil Green's SWAT, Cross_Match, and Phrap programs. SPSOFT has modified these applications for optimal performance on single and multi-CPU computer systems. See our Support page for information on supported operating systems.
SPS Phrap has been optimized to run faster on a single processor and can scale well as processors are added to a job.
SPS Phrap can dramatically reduce the time it takes to run tough phrap jobs. Our tests demonstrate a 7.2x performance improvement with 8 CPUs. On 2 processor systems, SPS Phrap runs 2.5x faster than UW Phrap v.960731.
SPS SWAT is a scalable version of the Smith-Waterman algorithm. SPS SWAT supports linear (affine) gap penalties. It scales linearly as CPUs are added to a job. SPS SWAT scaled 19 times on a 20 processor Sun Ultra Enterprise server.
Description of Cross_Match (from Phil Green's documentation):
SPS Cross_Match runs up to 30% faster than the original Cross_Match when run with a single CPU. SPS Cross_Match runs 3 times faster on a 4 CPU system. SPS Cross_Match has been optimized to work with all-to-all comparisons.
SPSpfam is a plug-in replacement for Sean Eddy's Hmmpfam module from Hmmer. It provides a significant performance gain over Hmmpfam across the whole spectrum of input query characteristics. For performance comparisons see
SPSsearch is a refined search replacement for NCBI BLAST. It provides all of the BLAST frame search options with a single or double affine Smith-Waterman alignment algorithm. For the command options see
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