    TeXshade v1.24
    >>
    >> 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 - 2011  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.
