--{- Genetic Analysis System -}-- (original) (raw)

GAS is an integrated computer program designed to automate and accelerate the acquisition and analysis of genomic data. It was primarily developed byDr. Alan Youngworking atOxford University.

Y2K - GAS is believed to be fully Y2K compliant provided that the system clock works correctly on the host machine. On machines which are not themselves Y2K, the only problem will be an incorrect date stamp in the output files.

Linux - there is currently no free version of GAS available for Linux.

To retrieve the latest version of GAS (2.0) click on the appropriate icons below. The unpacking instructions given here may also be down-loaded as a README file.

This server is mirrored at

• Rockefeller (USA) If you have problems with WWW servers, GAS can also be obtained by anonymous ftp from:
• ftp.ox.ac.uk pub/users/ayoung
• linkage.cpmc.columbia.edu software/gas

Manuals

GAS2.0 comes with 2 manuals. These are in Postscript format (retrieve and save them as Ascii files) and should be printed on a Postscript compatible laserprinter:

• General User Guide
• Analysis Modules Whichever computer system you are using, you will need to download both of these manuals. Full instructions for installing and using the program and example files are given at the back of the General User Guide.

If you are unable to view/print Postscript files then anHTML version is available - however please read the caveats on the download page before atempting to use this.

PC DOS

For PC based systems, you require the file:

• IBM PC / DOS Once you have retrieved this file (as a binary image), typing `gas20dos' will automatically unpack both the GAS program and the example files. The package includes two auxillary files, 32RTM.EXE and DPMI32VM.OVL which you must install in the DOS path (the Windows directory must also be in the DOS path).

Unix Systems

You should load (as a binary image) the appropriate version of GAS for your system from the list below:

• DEC Alpha OSF
• DEC Ultrix
• Sun Solaris
• Sun OS
• Silicon Graphics IRIX
• IBM AIX

You will also require the example file package:

• compressed tar examples Once you have retrieved the appropriate files you can unpack them using the command:

zcat bundle.tar.Z | tar -xvf -

where bundle is the first part of the file name.

VMS Systems

You should load (as a binary image) the appropriate version of GAS for your system from the list below:

• DEC VAX
• DEC Alpha The VMS backup format may become corrupted during remote transfers and as a result there is not a specific example file package for VMS. Instead please load either the Unix or DOS example packages, the contents of which are identical.

Problems

There are 2 known problems with version 2.0

• The sibmwu() routine may return negative p-values in cases where the 0-sharers are more similar than the 1-sharers. Since these cases are of no interest to gene identification, the spurious results may be ignored.
• The pscontrol parameter smoothfactormay fail unless it has a value equal to (or greater than) the number of points from which the interpolation is made.

Vitesse

GAS uses Jeff O'Connell's Vitesse routines to perform the likelihood calculations in the lik*() routines. TheVitesse packageis also available as a stand-alone program.

Support

GAS is no longer actively supported by the author. If you wish to obtain help on using it then please try relevant news/usergroups.

Bugs may still be reported however, and if sufficiently serious (i.e. affecting numerical results rather than aesthetic presentation) will be posted in the Problems section above.

A version of GAS for Linux is frequently requested. However as the author has moved to working inclinical trials/epidemiologythis would have to be developed outside the academic framework and require external funding. Feel free to get in touch if you have such funding.

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