Index of /downloads/alscript

	Name	Last modified	Size	Description
	Parent Directory		-
	LICENSE	2000-03-23 11:13	5.4K
	alscript_2.07d.tar.gz	2011-08-02 14:10	2.9M
	bobscript_colour_def..>	1998-08-10 18:11	1.3K
	old_versions/	2011-08-02 14:12	-

This directory contains a gzip tar file of alscript.2.07 and a 

   Barton, G. J. (1993)
   ALSCRIPT a tool to format multiple sequence alignments
   Protein Engineering, Volume 6, No. 1, pp.37-40.

ALSCRIPT will compile and run on most computers that have an ANSI-C
compiler.  Makefiles are included for Sun, Silicon Graphics and VAX/VMS, but
in 2011 the only one I know works for sure is makefile.linux.  This can be
used for cygwin and linux installation. 

Brief Description of ALSCRIPT
-----------------------------

ALSCRIPT takes a multiple sequence alignment in AMPS (Barton &
Sternberg, 1987, Barton, 1990) block-file 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.

Given a block-file and pointsize (character width/height), ALSCRIPT
calculates how many  residues can be fitted across the page, and how
many sequences will fit down the page, it then  prints the  alignment at
the chosen pointsize on as many pages as are needed.  Running ALSCRIPT  with
a smaller or larger pointsize will automatically re-scale the alignment
to fit on fewer or more pages as appropriate.  The actual page
dimensions may be re-set to any value, so if you  have access to an A3
PostScript printer, or typesetting machine, alignments can readily be
scaled to maximise the available space.

Each output page has three basic regions.  The left hand edge contains
identifier codes for each sequence.  The main part of the page holds the
alignment, and the top part, the position numbers and tick marks.  ALSCRIPT
commands make use of a character coordinate system for font  changes,
and other formatting commands. Thus, any residue  in the alignment may
be referred to by its sequence  position number (x-axis) and sequence
number  (y-axis), similarly, ranges of residue positions, or sequences
may also be defined in the  character coordinate system.

The basic ALSCRIPT commands allow the following functionality:

Fonts:  Any PostScript font at any size may be defined and used on
individual residues,  regions or identifier codes.

Boxing: Simple rectangular boxes may be drawn around any part of the
alignment.  Particular  residue types may be selected and automatically
"surrounded" by lines.  For example, if the  characters 'G' and 'P' are
selected, then lines will not be drawn between G and P characters,  but
only where G and P border with other characters.

Shading:  Grey shading of any level from black to white may be applied
to any region of the  alignment, either as a rectangular region, or as
residue specific shading.  e.g. "shade all Cys residues between
positions 6 and 30" 

Text:  Specific text strings may be added to the alignment at any
position and in any font or font size.

Lines: Horizontal or vertical lines may be drawn to the left, right, top
or bottom of any  residue position or group of positions.

Colour:  Characters or character backgrounds may be independently
coloured.