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authorNorbert Preining <norbert@preining.info>2019-09-02 13:46:59 +0900
committerNorbert Preining <norbert@preining.info>2019-09-02 13:46:59 +0900
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+ TeXshade v1.25
+ >>
+ >> A LaTeX package for setting nucleotide and peptide alignments,
+ >> fingerprints, as well as sequence and subfamily logos.
+ >>
+ >> 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 - 2018 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)
+ AQP_TC.asc Example T-Coffee shading file
+ AQP2spec.ALN Example protein alignment file (ALN-format)
+ AQP1.top Example topology data file generated from PHD
+ AQP1.phd Example PHD secondary structure file
+ AQP1_HMM.sgl Example HMMTOP topology data (single line format)
+ AQP1_HMM.ext Example HMMTOP topology data (extended format)
+ 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: ebeitz@pharmazie.uni-kiel.de
+ WWW: http://www.pharmazie.uni-kiel.de/chem/
+ (On-line documentation and updates)
+ Address: Eric Beitz, University of Kiel, Pharmaceutical Chemistry,
+ Gutenbergstrasse 76, D-24118 Kiel (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.