    TeXshade v1.29
    >>
    >> 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 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 - 2025  Eric Beitz




1 - FILES DISTRIBUTED WITH THIS PACKAGE

    texshade.ins		Batch file, run through LaTeX
    texshade.dtx		Docstrip archive, run twice through LaTeX
    README		This file

    
  (a) FILES THAT WILL BE GENERATED BY RUNNING 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)
    AQP_sequence_logo_1FX8.cmd
                   		Example structure meme file
    AQP_subfamily_logo_1FX8.cmd
                   		Example structure meme file
    meme.eps 		Meme output graphics example
    frustr.txt			local frustration example file
    bars.txt stacked	bars example file
    Standard.cod	Standard genetic code definitions
    Ciliate.cod		Ciliate macronuclear genetic code definitions


  (b) FILE THAT WILL BE GENERATED BY RUNNING TEXSHADE.DTX

    texshade.pdf   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).


  (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.
    
    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.



3 - CONTACT

    E-Mail:		ebeitz@pharmazie.uni-kiel.de
    WWW:		https://www.pharmazie.uni-kiel.de/en/pharmceitica/prof-dr-eric-beitz/biotex
    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.