Additional molecular biology software supported by ACHS

A list of sequence analysis programs that are maintained locally.

Supported Programs

GCG sequence analysis package

PHYLIP phylogenetic package and information on other phylogenetic packages. EMBOSS package, with embassy additions T-Coffee, (also available on-line at EMBL and CNRS)

ClustalW and ClustalX (ClustalW is also available at many web sites - Google will quickly fine them for you)

Readseq A useful utility to convert sequence formats.

Unsupported programs

S.A.G.E. 5.0 - Statistical Analysis for Genetic Epidemiology (manual). This program is installed on opus.achs.virginia.edu and is available to ACHS account holders (ie. if you have an account on watson.achs.virginai.edu, or have a SeqWeb account, then you also have an account on opus). Only one user may run S.A.G.E. at any given time. Windows users will need to login to opus using eXceed (see instructions here). Mac OS X users will need Apple's X11 (see information here). The command to connect would be:

ssh -X -l your_UVa_user_id opus.achs.virginia.edu

Alscript Shades and boxes multi sequence alignments. This program is very difficult to use and it takes a significant amount of time to get the output adjusted, but the results are impressive. Examples.

Alscript uses text files (control files) as script templates for conversion of alignments to postscript language files. It is a command line program only.

AlScript ver. 2.04 (28 June 1996) runs on watson.achs.virginia.edu at the >GCG> shell prompt. Just type alscript and it will prompt you for an Alscript Command file name (which can be generated in any UNIX test editor). An online manual is available on the developer's web site, here.

Alscript can be obtained from the author, Dr. Geoff Barton, via his web site at the University of Dundee. It is available for Intel 386 machines running Windows 95 or 98, a few UNIX systems (the SunOS 4.1.3 version should run on watson.achs.virginai.edu if you download it to your home directory), and as source code.

For those looking for alternatives to Alscript for making colour alignments, please go to this page.

Please email comments or suggestions about the ACHS MolBiol pages to mblack@virginia.edu.

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