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TeXshade v1.12
>>
>> A LaTeX package for setting nucleotide and peptide alignments.
>>
>> Setting alignments of nucleotides and peptides for publication
>> or presentation purposes is usually a time consuming two-step
>> process. First, a scientific software is used for the calcula-
>> tion of the alignment. This is done in a few minutes. Then, in
>> order to highlight special sequence relationships and to label
>> positions and regions of interest a second software with high
>> output capability is needed.
>>
>> Manipulating sequence alignments with standard word processing
>> or graphics programs takes its time--often several hours--and
>> simple layout changes such as re-breaking lines, say from 50
>> to 40 residues per line, elongate the working time considerab-
>> ly.
>>
>> TeXshade is an alignment shading software completely written
>> in TeX/LaTeX which can process multiple sequence alignments in
>> the MSF, ALN and FASTA file format. It provides in addition to
>> common shading algorithms special shading modes featuring
>> functional aspects, e.g. charge or hydropathy, and a plenitude
>> of commands for handling shading colors, text styles, labels,
>> legends and even allows the user to define completely new sha-
>> ding modes. TeXshade combines highest flexibility and the
>> habitual TeX output quality--with reasonable time expenditure.
>>
Copyright (C) 1999 - 2005 Eric Beitz
FOR THE HASTY READER
Be sure to use a docstrip version 2.4 or later!
Otherwise you will not be able to tex the documentation!
1 - FILES DISTRIBUTED WITH THIS PACKAGE
texshade.ins Batch file, run through LaTeX
texshade.dtx Docstrip archive, run twice through LaTeX
tsfaq.tex Frequently asked questions about TeXshade
texshade.txt This file
(a) FILES THAT WILL BE GENERATED FROM TEXSHADE.INS
texshade.sty LaTeX package
texshade.def Standard definitions
AQPDNA.MSF Example nucleotide alignment file (MSF-format)
AQPpro.MSF Example protein alignment file (MSF-format)
AQP2spec.ALN Example protein alignment file (ALN-format)
AQP1.top Example topology data file generated from PHD
AQP1.phd Example PHD secondary structure file
Standard.cod Standard genetic code definitions
Ciliate.cod Ciliate macronuclear genetic code definitions
(b) FILE THAT WILL BE GENERATED FROM TEXSHADE.DTX
texshade.dvi Package documentation
2 - INSTALLATION
(a) EXTRACTING FILES FROM THE DOCSTRIP ARCHIVE
All files provided by TeXshade are compacted to one single file,
namely "texshade.dtx". To extract the archive run "texshade.ins"
- which contains the corresponding instructions - through LaTeX.
A list of the generated files is given above, see 1(a).
AGAIN: Be sure to use a docstrip version 2.4 or later! Otherwise
you will not be able to tex the documentation!
(b) THE DOCUMENTATION
The file "texshade.dtx" further contains the package documentation.
Therefore, run this file through LaTeX now. As you will recognize
two runs are needed to make proper references within the document.
TeXshade needs lots of TeX's memory, so adjust your parameter set-
tings to make TeXshade feel comfortable. The documentation is a
good test for this. (If you encounter problems texing the doc, you
should tex and read section A of the FAQ-list (see d below) or
download an on-line version [PDF-, DVI-, or PostScript format] at
http://homepages.uni-tuebingen.de/beitz/)
The resulting file "texshade.dvi" can be viewed and printed using a
DVI-viewer which is able to display embedded PostScript. Another
possibility is to run "texshade.dvi" through DVIPS, a DVI to Post-
Script converter, and finally view and print the converted file
which will be most likely "texshade.ps" with GhostView from the GNU
free software foundation.
TeXshade makes use of "color.sty" by David Carlisle. This style is
part of the Standard LaTeX Graphics Bundle. Usually, the bundle is
present in a comprehensive LaTeX installation. If this is not the
case for your system you have to download the package from a CTAN-
server, e.g. ftp.dante.de.
(c) MAKING TEXSHADE.STY AVAILABLE FOR YOUR LATEX SYSTEM
In the final step, copy at least the files "texshade.sty" and
"ciliate.cod" to a directory searched by TeX in order to make these
files available for all documents you'll produce in the future. The
remaining files are example files which are not necessary for run-
ning TeXshade. Nevertheless, it would be a good idea to keep all
the files together.
(d) THE FAQ LIST
The FAQ list contains frequently asked questions about the package.
Use it as a helpful source for solving problems with TeXshade. You
get the list by simply running "tsfaq.tex" through LaTeX once.
3 - CONTACT
E-Mail: eric.beitz@uni-tuebingen.de
WWW: http://homepages.uni-tuebingen.de/beitz/
(On-line documentation and updates)
Address: Eric Beitz, Universit"at T"ubingen, Pharmazeutische Chemie,
Auf der Morgenstelle 8, D-72076 T"ubingen (Germany)
4 - AGREEMENT
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
In order to receive a copy of the GNU General Public License write to
the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
Boston, MA 02111-1307, USA.
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