ALSCRIPT: ALignment -> postSCRIPT

Description

From the ALSCRIPT manual:

ALSCRIPT takes a multiple sequence alignment in AMPS (Barton & Sternberg, 1987, Barton, 1990) blockfile format and a set of formatting commands and produces a PostScript file that may be printed on a PostScript laser printer, or viewed using a PostScript previewer (e.g. Sun Microsystem's PageView program). CLUSTAL and GCG format multiple alignment files may also be used (see below). ALSCRIPT is NOT a multiple sequence alignment program, nor is it an alignment editor.

The CSB has installed ALSCRIPT Version 2.07a.

License and Credits

Alscript is licensed from the author. The license reads, in part,

All credits and copyright notices in the WORK, both in listings and/or documentation, whether names of individuals or organisations, shall be retained in place. Publications referring to the WORK, or to other works containing the WORK in whole or in part, shall refer to it as ALSCRIPT and shall specify that the WORK was made by Geoffrey J. Barton. Publication of results that use the WORK shall cite: Barton, G. J. (1993), Prot. Eng., 6, 37-40.

Read the full license.

The Alscript web page can be found at www.compbio.dundee.ac.uk /Software/Alscript/alscript.html

top docs run alscript examples sysadm

ALSCRIPT Documentation

Alscript manual in PDF format.

Alscript manual in Postscript format. This is probably set up for A4 paper, and may not easily print on our printers.

Online ALSCRIPT documentation (Version 2.03).

Running ALSCRIPT

Alscript is currently installed on Core linux computers. Set your path by typing,

setup alscript

Now, invoke the program by typing,

alscript

The program will tell you:

Enter ALscript Command File name:

Type in the name of your .als file (described in the program documentation).

top docs run alscript examples sysadm

Examples

ALSCRIPT examples can be found in /srv/local/alscript/demo You will find three types of files there:

*.blc input data in blockfile format
*.als formatting commands for ALSCRIPT
*.ps Postscript output from the examples

Copy the example files to your directory. Run alscript, and enter the name of a .als file when it asks for the Alscript Command File Name.

System Administration

Installation notes are found here.

top docs run alscript examples sysadm

Last Modified: Wednesday, 02-Feb-2005 14:00:55 EST

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Richards Center (www.rc.yale.edu) at Yale University (www.yale.edu)
Contact: michael^strickler_at_yale^edu

*.blc	input data in blockfile format
*.als	formatting commands for ALSCRIPT
*.ps	Postscript output from the examples