Software

Software and Manuals


	Here you can find manuals for Barton Group Software that was principally developed in Oxford (AMPS, AMAS, ALSCRIPT, STAMP, MAP, ASSP, SCANPS, OC and DOMAK). As of the 1st August 1998, the ownership of this software has now passed to the developers. To register for any of these programs, please see this page.

(click image to register)

The ALSCRIPT User Guide (Version 2.0). Alscript is a program to format multiple sequence alignments in PostScript. For details see: Barton, 1993. The manual for the previous version of ALSCRIPT is also available.

The AMPS (Alignment of Multiple Protein Sequences) User Guide. AMPS is a suite of programs for multiple sequence alignment. The programs include options to incorporate non-sequence information such as secondary structures. AMPS also implements flexible pattern matching and database scanning options.

The SCANPS Version 1 protein database scanning package - User Guide. SCANPS is a program for rigorous database scanning using a derivative of the Smith-Waterman algorithm. It is fast enough to use routinely on a workstation and is currently available in binary form for Sun and Silicon Graphics. You can download the package from our distribution page. See Barton (1992a) for a short discussion of computer speed and database size.

For fast database searching on multiprocessor or uniprocessor computers, more flexibility in file formats as well as DNA scanning, try Version 2

The SCANPS VERSION 2 protein and DNA sequence scanning package - User Guide.SCANPS version 2 takes full advantage of Silicon Graphics multiprocessor computers to give fast database searching. The program implements Smith-Waterman with and without affine gaps as well as DNA versus protein searching that allows for frameshift errors. The fastest algorithm implemented achieves over 700 million array operations per second on a 24 processor Silicon Graphics Challenge R10000.
Look at the distribution page to download the scanps 2.X program. A database searching service that uses scanps is available.

The AMAS Analysis of Multiply Aligned Sequences - User GuideandAMAS Server.

AMAS is a program to analyse multiple alignments of protein sequences. It allows the identification of functional residues by comparison of sub-groups of sequences arranged on a tree. Also see the Java program JalView that implements many of the ideas from AMAS.

The STAMP (VERSION 4.0) Structural Alignment of Multiple Proteins User Guide. A Postscript copy of this manual is also available for printing on A4 or US Letter paper.

The DOMAK (Version 1.2) Domain identification program. DOMAK defines domains in protein 3D structures given a set of x,y,z coordinates for the protein.

The OC Cluster analysis program. OC implements single, complete and means linkage cluster analysis. It does not have software limits on the number of entities that can be clustered.
See the distribution page to download this program.