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diff --git a/Master/texmf-dist/doc/latex/texshade/README b/Master/texmf-dist/doc/latex/texshade/README new file mode 100644 index 00000000000..752a63a8538 --- /dev/null +++ b/Master/texmf-dist/doc/latex/texshade/README @@ -0,0 +1,149 @@ + 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. |