The Sequence Alignment and Modeling (SAM) software suite is written in ANSI C for Unix workstations. Additionally, we have implemented the inner loop in MPL for the MasPar family of parallel computers. The system has been tested on DEC Alpha, Decstation, IBM RS/6000, SGI, and Sun Sparc workstations. The research described herein was performed on a Sun Sparc 30/10 and a MasPar MP-2204 connected to a DEC Alpha 5000/300.
Newly revised and documented workstation and MasPar versions of SAM are available from our WWW site, http:/www.cse.ucsc.edu/research/compbio/sam.html. We recently created a server for using SAM to align and model sequences, which is accessible from the SAM WWW page. Questions concerning the software and its distribution can be mailed to sam-info@cse.ucsc.edu.