%    \iffalse
%
% texshade.dtx
% Docstrip archive,  to extract documentation  run twice through 
% LaTeX.
% To  successfully  extract the documentation it is necessary to
% first run the file `texshade.ins' through LaTeX. This produces 
% the needed style  file  `texshade.sty'  and the parameter file
% `texshade.def' as well as several example files.  See the file
% `texshade.txt' for further information!
% 
%
% Copyright (C) 1999-2008 Eric Beitz
% See the file texshade.txt
% 
%    \fi
%
%    \changes{1.0}{1999-5-12}{First release}
%    \changes{1.1}{1999-5-26}{%
%      Corrections:  `emphregion'  is not extending to the next
%                                  alignment any more;
%                    `namecolor' & `numbercolor' are now correctly
%                                                reordered;
%                    sequence gaps at the beginning or the end are
%                    now treated correctly, i.e. no symbols are shown.
%      Introduction: `seqlength'
%                    `gapcolors'
%                    `rulersteps'
%                    `hideresidues'
%                    `showresidues'
%                    `fingerprint'.}
%    \changes{1.2}{1999-6-12}{%
%      Corrections:  functional shading error in funcgroup no. 8.
%      Introduction: `includeDSSP'
%                    `includeSTRIDE'
%                    `includePHDsec'
%                    `includePHDtopo'
%                    `appearance'
%                    `numcount'
%                    `alphacount'
%                    `Alphacount'
%                    `showonDSSP'
%                    `hideonDSSP'
%                    `showonSTRIDE'
%                    `hideonSTRIDE'
%                    `showonPHDsec'
%                    `hideonPHDsec'
%                    `showonPHDtopo'
%                    `hideonPHDtopo'.}
%    \changes{1.2a}{1999-6-24}{%
%      Corrections:  `namecolor' & `numbercolor' are now really
%                                                correctly reordered;
%                    in sequence names ( and ) are now allowed;
%                    option `case' in `funcshadingstyle' works now.}
%    \changes{1.3}{2000-3-3}{%
%      Corrections:  features in the ttop row do not produce line
%                                                scrambling any more;
%                    `language' replaced by `germanlanguage'
%                                       and `englishlanguage' due to
%                                       incompatibilities with babel;
%                    incompatibility with amsmath's text command fixed.
%      Introduction: new feature option `translate'
%                    `codon'
%                    `geneticcode'
%                    `backtranslabel'
%                    `backtranstext'
%                    `romancount'
%                    `Romancount'
%                    TeXtopo compatibility.}
%    \changes{1.3a}{2000-7-28}{%
%      Introduction: `showleadinggaps'
%                    `hideleadinggaps' to hide or show gap symbols 
%                                      before the actual seq start.}
%    \changes{1.3b}{2000-7-30}{%
%      Corrections:  `showleadinggaps'
%                    `hideleadinggaps' were extended to `ending' gaps;
%                    sequence names input routine now accepts special 
%                    characters.}
%                    
%    \changes{1.4}{2000-9-12}{%
%      Introduction: `movelegend'  allows one to move the legend;
%                    series of sequence numbers, e.g. in `orderseqs',
%                    can now be written with a dash, e.g. {1-3,6-4,7} instead
%                    of {1,2,3,6,5,4,7}.}
%
%    \changes{1.4a}{2000-10-3}{Documentation and FAQ additions}
%    
%    \changes{1.5}{2001-02-22}{%
%      Corrections:  `X's in the alignment lead to a run-time error;
%      Introduction: `ttopspace'
%                    `topspace'
%                    `bottomspace'
%                    `bbottomspace' for controlling vertical space 
%                                   between feature lines.
%                    `showcaption'  for adding a caption to the alignment.
%                    the sequence lengths are now stored in the .aux 
%                    in order to have correct gap breaks after the seqs.}
%                    
%    \changes{1.5a}{2001-03-08}{%
%      Corrections:  Eckhart Guth\"orlein noticed a sorting problem 
%                    when in addition some sequences where `killed' and
%                    the consensus was set to a particular sequence.
%                    This update fixes this problem.}
%                    
%    \changes{1.6}{2002-03-26}{%
%      Corrections:  There is no restriction to `dvips' anymore. One
%                    can add an option to the \usepackage{texshade}
%                    call which is passed to color.sty, e.g. `dvipdf';
%                    `noblockskip' led to over-printing of lines;
%                    `namecolor' and `numbercolor' did not support 
%                    sequence lists - fixed (thanks to Denys Bashtovyy).
%      Introduction: The FASTA file format is now supported;
%                    references to sequences can be made by name in
%                    addition to number;
%                    sequences can be refered to by their name in 
%                    addition to their number in the input file
%                    (suggested by Christoph Gille);
%                    `flexblockspace'   optimizes the space between 
%                                       sequence blocks to be minimal (is
%                                       default as before);
%                    `fixblockspace'    leads to an equal separation of
%                                       sequence blocks independent of
%                                       feature lines;
%                    `firstcolumnDSSP'  lets you choose the first numbering
%                                       column in DSSP input files and
%                    `secondcolumnDSSP' the second column.}
%                    
%    \changes{1.7}{2004-01-05}{%
%      Corrections:  Several bugs were fixed.
%                    In gaps the wrong character was plotted in `donotshade'
%                    mode. Gaps were colored incorrectly when a single 
%                    sequence was set as consensus. (thanks to Jeferson J. 
%                    Arenzon). Another `donotshade' problem was solved 
%                    which led to a halt of the LaTeX run (thanks go to
%                    Naomi Siew). The gap and match labels in diverse
%                    mode were switched (`-' in gaps; `.' at matching
%                    positions) in order to follow convention.
%      Introduction: Spanish labels (contributed by Mikel Egana Aranguren);
%                    New feature label `helix'.}
%   
%    \changes{1.8}{2004-08-26}{%
%      Corrections:  Minor bugs were fixed.
%      Introduction: Definition of "light" versions of all colors;
%                    Definition of three color ramps: 
%                        Red-Blue, Green-Red and Cold-Hot;
%                    New feature labels `bar' and `color'.}
%   
%    \changes{1.9}{2005-02-08}{%
%      Corrections:  Fixed TeXtopo incompatibility introduced with v1.8.
%                    (Thanks to Meike Schmedt)
%      Introduction: Implementation of HMMTOP topology prediction.                   
%                    `includeHMMTOP'
%                    `showonHMMTOP'
%                    `hideonHMMTOP'
%                    new `appearance' option {HMMTOP} with {internal}
%                                                          {external}
%                                                          {TM};
%                    new arrow look with scalable line thickness;
%                    new arrow option `ball';
%                    `frameblock'   colored frame around sequence block;
%                    `shortcaption' allows one to define short caption
%                                   versions for the List of Figures.}
%
%    \changes{1.10}{2005-03-29}{%
%      Corrections:  Sped up drawing of color scales and bar graphs by
%                    by more than 10fold!
%                    (Thanks, Christoph Gille, for asking for it)
%      Introduction: Definition of even lighter versions of all colors;
%                    implementation of a new labeling mode 'tint':                   
%                    `tintregion'
%                    `tintblock'
%                    `tintdefault';
%                    new `feature' option {restriction} for putting a
%                    triangle label pointing between two residues;
%                    data files for color scales and bar graphs can
%                    now contain 'NaN' (not a number) values
%                    (Also requested by Christoph Gille.)}
%
%    \changes{1.11}{2005-04-13}{%
%      Corrections:  Frames were drawn with the wrong height when
%                    separation lines were used. Fixed.
%                    Spacing between bar graph feature line and 
%                    sequence block was wrong after `bargraphstretch'.
%      Introduction: Additional optional parameter for feature rule
%                    thickness;                   
%                    additional optional parameters for feature box
%                    frame color and frame thickness;
%                    definition of three more color scales:
%                    {RedBlue}, {RedGreen}, and {HotCold};
%                    plotting of amino acid features as bar graphs
%                    or color scales:
%                    `hydrophobicity'
%                    `molweight'
%                    `charge';
%                    plotting of protein sequence conservation as
%                    bar graph or color scale:
%                    `conservation';
%                    separate command for stretching color scales:
%                    `colorscalestretch';
%                    color scales on consensus sequence according
%                    to sequence conservation.
%                    }
%
%    \changes{1.12}{2005-09-20}{%
%      Corrections:  Combination of 'setends' with regional labeling
%                    using 'shaderegion', 'frameblock', 'emphregion'
%                    or 'tintregion' produced incorrect output
%                    (thanks to Chris Page). Fixed.
%      Introduction: Optional colors for `showconsensus' foreground
%                    and background.
%                    }
%
%    \changes{1.13}{2006-02-23}{%
%      Corrections:  Helix symbols in feature lines were not drawn
%                    correctly if the standard Computer Modern Font
%                    was changed to another one, e.g. Palatino (thanks
%                    to Markus Heller). Fixed.
%                    Unintended gaps occurred due to numbers at the
%                    end of lines in Clustal W alignment files. Fixed.
%                    Frames were too tall when sequences were hidden
%                    or killed. Fixed.
%                    The limitations in the number of sequences per
%                    alignment have finally been overcome by a more
%                    restrictive use of counter variables.
%      Introduction: The numbering can now be displayed on both sides
%                    of the alignment with the optional parameter
%                    {leftright};
%                    TeXshade tries to guess the sequence type (protein 
%                    or nucleotide) if not defined by the user;
%                    Implementation of sequence logos:
%                    `showsequencelogo', `hidesequencelogo', 
%                    `namesequencelogo', `logostretch',
%                    `logocolor', `clearlogocolors',
%                    `showlogoscale', `hidelogoscale'
%                    `dofrequencycorrection', `undofrequencycorrection';
%                    The ruler numbering can now be rotated with
%                    `rotateruler' and back with `unrotateruler',
%                    this way every position can be numbered which is
%                    often wanted when e.g. sequence logos are plotted;
%                    the font family (sf, rm, tt) can be set for the
%                    ruler, e.g. `rulertt' or `setfamily{ruler}{tt}';
%                    `hideseqs' and `showseqs' in order to hide/show
%                    all sequences, esp. useful with sequence logos;
%                    `allowzero' and `disallowzero' - use (or do not 
%                    use) the number `0' in the sequence numbering as
%                    sometimes wanted in sequence logos;
%                    Implementation of a new way to visualize residues  
%                    which are characteristic for protein subfamilies, 
%                    i.e. subfamily logos:
%                    `showsubfamilylogo', `hidesubfamilylogo', 
%                    `namesubfamilylogo', 
%                    `setsubfamily', 
%                    `shownegatives', `hidenegatives'.
%                    }
%
%    \changes{1.14}{2006-05-11}{%
%      Introduction: `showrelevance', `hiderelevance',
%                    `relevance': commands to set a bit-value above
%                    which subfamily deviations are considered relevant
%                    and to label such positions in the subfamily logo.
%                    }
%
%    \changes{1.15}{2006-06-27}{%
%      Correction:   Logos can now be plotted with pdflatex; pstricks is
%                    not needed anymore.
%                    }
%
%    \changes{1.16}{2007-02-18}{%
%      Corrections:  TeXshade crashed when doing conservation
%                    calculations with sequences containing untypical
%                    residues symbols, such as X. Fixed.
%                    Shading of the reference sequence in diverse mode
%                    is now achieved with `conservedresidues' and
%                    `allmatchresidues' instead of `nomatchresidues'.
%      Introduction: `exportconsensus' produces a pymol script for
%                    coloring according to the TeXshade conservation
%                    calculation;
%                    `namerulerpos' allows one to change labels of
%                    the ruler individually;
%                    `hideblock' allows one to hide parts of the
%                    alignment (still in experimental stage!).
%      New home:     TeXshade, TeXtopo, and BioTeX have a new home:
%                    `www.pharmazie.uni-kiel.de/chem/Prof_Beitz/biotex.html'
%                    }
%
%    \changes{1.17}{2007-06-19}{%
%      Corrections:  .
%      Introduction: `allmatchspecial' now accepts an optional threshold
%                    percentage allowing one to set two levels off 
%                    conservation;
%                    the same effect can be achieved by using a
%                    number as an optional parameter in
%                    `shadingmode',
%                    or by setting an additional parameter in 
%                    `threshold';
%                    names can be displayed left or right of feature
%                    lines using:
%                    `showfeaturename', `showfeaturestylename';
%                    `hidefeaturename', `hidefeaturestylename';
%                    `hidefeaturenames', `hidefeaturestylenames';
%                    the color of such names can be changed with
%                    `featurenamescolor'
%                    `featurestylenamescolor'
%                    font styles can be set as usual, e.g.
%                    `setsize{featurenames}{large}' or
%                    `featurestylenamesrm' etc.
%                    }
%
%
%    \changes{1.18}{2008-04-15}{%
%      Corrections:  bug fixes concerning:
%                        featurenames, ordering, numbering, setends.
%      Introduction: T-Coffee shading can be imported and displayed 
%                    in the alignment, in the consensus, 
%                    in feature color scales and bar graphs by 
%                    `shadingmode[ASCII-file]{T-Coffee}' and
%                    `includeTCoffee';
%                    two more feature lines on top and at bottom:
%                    `ttttop', `tttop', `bbbottom', and `bbbbottom';
%                    fusion of the `startnumber' and `setends' commands
%                    via optional parameters.
%                    }
%
%
%
%
% \CharacterTable
%  {Upper-case    \A\B\C\D\E\F\G\H\I\J\K\L\M\N\O\P\Q\R\S\T\U\V\W\X\Y\Z
%   Lower-case    \a\b\c\d\e\f\g\h\i\j\k\l\m\n\o\p\q\r\s\t\u\v\w\x\y\z
%   Digits        \0\1\2\3\4\5\6\7\8\9
%   Exclamation   \!     Double quote  \"     Hash (number) \#
%   Dollar        \$     Percent       \%     Ampersand     \&
%   Acute accent  \'     Left paren    \(     Right paren   \)
%   Asterisk      \*     Plus          \+     Comma         \,
%   Minus         \-     Point         \.     Solidus       \/
%   Colon         \:     Semicolon     \;     Less than     \<
%   Equals        \=     Greater than  \>     Question mark \?
%   Commercial at \@     Left bracket  \[     Backslash     \\
%   Right bracket \]     Circumflex    \^     Underscore    \_
%   Grave accent  \`     Left brace    \{     Vertical bar  \|
%   Right brace   \}     Tilde         \~}
%   
%
%    \newsavebox{\mybox}
%    \newenvironment{fmpage}[1][0.975\textwidth]{%
%       \begin{lrbox}{\mybox}\begin{minipage}{#1}}
%      {\end{minipage}\end{lrbox}\fbox{\usebox{\mybox}}}
%        
%    \parindent0mm
%            
%     
%    \title{The \TeXshade{} package\footnote{Please cite: Eric Beitz (2000), 
%           \TeX{}shade: 
%           shading and labeling multiple sequence alignments using \LaTeXe. 
%           \textit{Bioinformatics}: \textbf{16}, 135--139.}\\[2mm] \large
%           Typesetting \\ nucleotide and peptide alignments}
%    \author{Eric Beitz\footnote{University of Kiel, 
%            Pharmaceutical Chemistry, Gutenbergstrasse 8, 
%            D-24118 Kiel, Germany; 
%            send electronic mail to \texttt{ebeitz@pharmazie.uni-kiel.de};
%            for further information, updates and on-line documentation 
%            see my homepage at
%            \texttt{www.pharmazie.uni-kiel.de/chem/Prof\_Beitz/biotex.html} }}
%    \date{v1.18; 2008/04/15\\}
%    \maketitle
%    \begin{abstract}
%      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 calculation 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 quality 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 considerably.
%      
%      \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 shading modes. \TeXshade{} 
%      combines highest flexibility and the habitual \TeX{} output 
%      quality---with reasonable time expenditure.
%      
%    \end{abstract}
%        
%    \thispagestyle{empty}
%    
%    \tableofcontents
%    \newpage
%    
%    \section{Package Overview}
%    
%    \label{over}
%   
%    After |texshade.ins| is run through \TeX{} the following files
%    should appear in the directory:
%    
%    \begin{tabbing}
%    \quad|texshade.sty|\quad\= the style file with all \TeXshade{} 
%                                      commands\\
%    \quad|texshade.def|\>      an example parameter file with the 
%                                      standard \\
%                              \>      parameter settings\\
%    \quad|AQPDNA.MSF|  \>      an example nucleotide alignment
%                                      (MSF-format)\\
%    \quad|AQPpro.MSF|  \>      an example protein alignment
%                                      (MSF-format)\\
%    \quad|AQP_TC.asc|  \>      an example T-Coffee shading file
%                                      (|score_ascii|-format)\\
%    \quad|AQP2spec.ALN|\>      a further protein alignment
%                                      (minimal ALN-file)\\
%    \quad|AQP1.phd|\>          secondary structure information
%                                      (PHD-format)\\
%    \quad|AQP1.top|\>          topology data extracted 
%                                      from |AQP1.phd|\\
%    \quad|AQP1_HMM.sgl|\>      topology information (single line,
%                                      HMMTOP-format)\\
%    \quad|AQP1_HMM.ext|\>      topology information (extended,
%                                      HMMTOP-format)\\
%    \quad|standard.cod|\>      standard genetic code definitions\\
%    \quad|ciliate.cod|\>       ciliate macronuclear genetic code\\
%    \end{tabbing}
%    The alignment file examples as well as the topology data file are 
%    needed for \TeX{}ing this documentation
%    and can serve as illustrations for the MSF and ALN 
%    file format.
%    
%    The following subsections give an overview on the capabilities of
%    the \TeXshade{} package. All commands are described in detail 
%    later on.
%    
%    
%    \subsection{Version History}
%
%    \textbf{v1.18 2008/04/15}
%    \medskip
%
%    \emph{Correction:} several bug fixed concerning featurename
%    display, sequence ordering and numbering.
%    
%    \emph{Introduction:}
%    (a) T-Coffee shading information can be loaded and put on the
%    alignment.\footnote{Suggestion by Florian Mertes.} 
%    The conservation data can also be displayed in the 
%    consensus as well as feature color scales and bar plots.
%    (b) Two more feature lines were added on the top and at the
%    bottom (|ttttop|, |tttop|, |bbbottom|, |bbbbottom|).
%    (c) The |startnumber| and |setends| commands have been fused;
%    either command can set both, a new start number as well as
%    end definitions of the sequence section to be displayed.
%    \bigskip
%
%    \newpage
%
%    \textbf{v1.17 2007/06/19}
%    \medskip
%    
%    \emph{Introduction:}\footnote{Asked for by Marat Kazanov.}
%    (a) A second threshold percentage was introduced in order to label
%    two levels of conservation in `identical' and `similar' mode. This is 
%    achieved by setting an optional parameter in |\threshold| or in 
%    |\allmatchspecial|, or by using a number as an optional parameter in 
%    |\shadingmode|. (b) The feature lines can be additionally labeled with
%    a name left or right of the feature. This is handled using
%    |\showfeaturename|, |\showfeaturestylename|,
%    |\hidefeaturename|, |\hidefeaturestylename|,
%    |\hidefeaturenames|, |\hidefeaturestylenames|.
%    The color of such names can be changed with
%    |\featurenamecolor|, |\featurestylenamecolor|,
%    |\featurenamescolor|, |\featurestylenamescolor|,
%    Font styles in feature names can be set as usual, e.g.
%    |\setsize{featurenames}{large}| or
%    |\featurestylenamesrm|.
%    \bigskip
%
%
%    \textbf{v1.17 2007/06/19}
%    \medskip
%    
%    \emph{Correction:} \TeXshade{} crashed when calculating conservation
%    using sequences with untypical residue characters, such as "X".
%    Fixed. The reference sequence in diverse mode can now be shaded with
%    |\conservedresidues| and, if active, |\allmatchresidues|.\footnote{For this
%    and suggesting |namerulerpos| credit to Marco Pasi.}
%
%    \emph{Introduction:}\footnote{Both extensions were suggested by Phillip Hahn.}
%    (a) A command was introduced, i.e. |\exportconsensus| 
%    which produces a pymol script file for coloring a 3D model according to 
%    \TeXshade{}s conservation calculation. (b) With |namerulerpos| labels of the
%    ruler can be exchanged by a string. (c) Various parts of the alignment 
%    can now be hidden by |\hideblock|. 
%
%    \emph{New home:} \TeXshade, \TeXtopo, and \BioTeX{} have a new home:
%    |www.pharmazie.uni-kiel.de/chem/Prof_Beitz/biotex.html|.
%    \bigskip
%
%
%    \textbf{v1.15 2006/06/27}
%    \medskip
%    
%    \emph{Correction:} Sequence and subfamily logos can now be plotted
%    with pdflatex; pstricks is not needed anymore.
%    \bigskip
%
%
%    \textbf{v1.14 2006/05/11}
%    \medskip
%    
%    \emph{Introduction:} In order to better recognize relevant positions
%    in a subfamily logo [14], a bit-value can now be set by |\relevance|
%    above which a deviation is considered relevant. Such positions
%    can be labeled with a symbol by |\showrelevance| and hidden
%    by |\hiderelevance|.
%    \bigskip
%
%
%    \textbf{v1.13 2006/02/23}
%    \medskip
%    
%    \emph{Corrections:} Helix symbols in feature lines were not drawn
%    correctly if the standard Computer Modern Font was changed to 
%    another one, e.g. Palatino.\footnote{Thanks to Markus Heller} 
%    Fixed. Unintended gaps occurred due to numbers at the
%    end of lines in Clustal W alignment files. Fixed. The limitations
%    in the number of sequences per alignment have finally been overcome
%    by a more restrictive use of counter variables.
%
%    \emph{Introductions:} (a) The numbering can now be displayed---in 
%    addition to left or right---on both sides of the alignment with 
%    the optional parameter |{leftright}| in the |\shownumbering| 
%    command (p.\pageref{Lshownumbering}). (b) TeXshade tries to guess 
%    the sequence type, i.\,e.\ protein or nucleotide, if not defined 
%    by the user. (c) Plotting of sequence logos has been implemented
%    (p.\pageref{Lshowsequencelogo}).
%    Logos can be shown in addition to or together with the consensus,
%    or alone without any alignment sequences. (d) The ruler numbering
%    can be rotated in order to make labeling of every position possible.
%    (e) A new way to visualize subfamily characteristics has been
%    implemented, i.e. subfamily logos (p.\pageref{Lshowsubfamilylogo}) [14].
%    \bigskip
%
%    \textbf{v1.12 2005/09/20}
%    \medskip
%    
%    \emph{Corrections:} When regional labeling with |\shaderegion|,
%    |\emphregion|, |\tintregion|, or |\frameblock| was combined with
%    |\setends| incorrect output was produced lacking the
%    labeling.\footnote{Discovered by Chris Page.} Other minor fixes.
%
%    \emph{Introductions:} An additional optional parameter for setting 
%    consensus colors was implemented in the |\showconsensus| command
%    (p.\pageref{Lshowconsensus}). This even allows one to use color 
%    scales illustrating sequence conservation in the consensus line.
%    \bigskip
%
%    \textbf{v1.11 2005/04/13}
%    \medskip
%    
%    \emph{Corrections:} Bounding boxes with |\frameblock| had a wrong
%    height when |\separationline|s were used. Other minor fixes.
%
%    \emph{Introductions:} (a) An additional parameter for setting 
%    individual bar and arrow thicknesses in feature lines has been 
%    introduced. (b) Additional parameters for setting the frame color
%    and thickness of boxes in feature lines have been implemented. (c)
%    Three more color scales have been defined: |RedBlue|, |RedGreen|,
%    and |HotCold|. (d) Plotting of amino acid features (|hydrophobicity|,
%    |molweight|, |charge|) as bar graphs or color scales. (e) Plotting
%    of protein sequence |conservation| as bar graph or color
%    scale\footnote{Ahmad Mirza asked for (e) and (f), great suggestion!}.
%    (f) Color scales can be used for shading the consensus sequence
%    according to protein sequence conservation.
%    (g) Separate command for stretching color scales |\colorscalestretch|.
%    \bigskip
%    
%    \textbf{v1.10 2005/03/29}
%    \medskip
%    
%    \emph{Corrections:} Plotting of color scales and bar graphs has
%    been sped up by more than a factor of 10.\footnote{This and (d)
%    I owe again to Christoph Gille.}
%
%    \emph{Introductions:} (a) More colors have been introduced, i.e. 
%    even lighter versions of the existing PostScript colors 
%    `LightLight' plus color name and `LightLightLight' plus color 
%    name. (b) Sequence stretches and blocks can be tinted for
%    labeling purposes |\tintreqion|, |\tintblock| and |\tintdefault|. 
%    (c) A new feature label style |{restriction}| has been introduced. 
%    (d) Java-typical `NaN' values are now allowed in data files for
%    bar graphs and color scales.
%    \bigskip
%    
%    \textbf{v1.9 2005/02/08}
%    \medskip
%    
%    \emph{Corrections:} \TeXshade{} version 1.8 introduced an
%    incompatibility with \TeXtopo{}. This problem was identified
%    by Meike Schmedt and has been fixed.
%
%    \emph{Introductions:} (a) A short version of the figure caption
%    can now be defined for display in the list of figures\footnote{%
%    Meike, here you go \dots} |\shortcaption{|\meta{text}|}|. (b) A
%    colored frame can be drawn around a sequence block for labeling
%    purposes with the command |\frameblock|.\footnote{Alan Robinson, 
%    this is for you.} (c) A new look for feature arrows has been 
%    implemented with scalable line thickness and a new end style
%    `ball'. (d) HMMTOP topology predictions can
%    now be included for plotting feature lines with information on
%    the location of the transmembrane domains.\footnote{Implemented 
%    after a request by Steffen Moeller.} 
%    \bigskip
%
%    \textbf{v1.8 2004/08/26}
%    \medskip
%    
%    \emph{Corrections:} Only minor bugs were fixed.
%
%    \emph{Introductions:} (a) More colors have been designed, i.e. 
%    `light' versions of the existing PostScript colors. (b) 
%    Three color ramps in 5\% steps have been introduced: 
%    i) Blue-Red, ii) Green-Red and iii) Cold-Hot.
%    (c) Two new feature label styles |bar| and |color| have been 
%    introduced which allow one to display number
%    values as bar graphs or color scales along the
%    alignment\footnote{Inspired by Christoph Gille's {\tt STRAP}}. 
%    \bigskip
%
%
%    \textbf{v1.7 2004/01/05}
%    \medskip
%    
%    \emph{Corrections:} Several bugs were fixed.
%    In gaps the wrong character was plotted in `donotshade'
%    mode. Gaps were colored incorrectly when a single 
%    sequence was set as consensus. Another `donotshade' problem was 
%    solved which led to a halt of the LaTeX 
%    run\footnote{Thanks to Jeferson J.\ Arenzon and Naomi Siew}. 
%    Due to several requests, the gap and match labels in |diverse|
%    mode were switched (`|-|' in gaps; `|.|' at matching
%    positions) in order to follow convention.
%
%    \emph{Introduction:} \TeXshade{} speaks spanish (|\spanishlanguage|).
%    Necessary translations were contributed by Mikel Ega\~na Aranguren.
%    A new feature label style |helix| has been introduced.
%    \bigskip
%
%    \textbf{v1.6 2002/03/26}
%    \medskip
%    
%    \emph{Corrections:} The unnecessary restriction to the DVIPS
%    driver for |color.sty| has been removed\footnote{As suggested by
%    Eckhart Guth\"ohrlein.}. Any color.sty compatible
%    driver option can be given with the |\usepackage{texshade}| call
%    and is then passed to the |color| package. The `|\namecolor|' and 
%    `|\numbercolor|' commands do now support sequence 
%    lists.\footnote{Thanks to Denys Bashtovyy.}
%        
%    \emph{Introductions:} (a) The FASTA file format is supported by
%    \TeXshade{} as alignment inputs. (b) Two commands set the space
%    between sequence blocks either to be flexible (as so far) 
%    `|\flexblockspace|' or the be fixed `|\fixblockspace|'. (c) One 
%    can now refer to sequences by their name in addition to the number
%    in the input file. (d) Using
%    `|\firstcolumnDSSP|' and `|\secondcolumnDSSP|' one can choose 
%    which of the first to columns should refer to the sequence numbering 
%    (the second column remains default setting)\footnote{c and d were
%    suggested by Christoph Gille.}.
%    \bigskip
%    
%    \textbf{v1.5a 2001/03/08}
%    \medskip
%    
%    \emph{Corrections:} `X's in the alignment file caused a run-time
%    error. Fixed.
%        
%    \emph{Introductions:} (a) The vertical space between feature
%    lines can be controlled by four new commands: |\ttopspace|,
%    |\topspace|, |\bottomspace| and 
%    |\bbottomspace|\footnote{Suggested by Ulrike Folkers.}. (b) It is 
%    now easily possible to add a caption to the alignment with 
%    the |\showcaption| command. (c) \TeXshade{} stores the 
%    sequence lengths in the |.aux| file in order to have correct
%    breaks of the gaps after the sequences.
%    \bigskip
%
%
%    \textbf{v1.4\&4a 2000/9/12 \& 2000/10/3}
%    \medskip
%    
%    \emph{Introductions:} (a) The alignment legend can now be moved 
%    by the command `|\movelegend|'. (b) In commands with parameters 
%    that contain series of sequence numbers, e.\,g. |\orderseqs|, a
%    dash can be used, e.\,g. |{1-3,6-4,7}| instead of 
%    |{1,2,3,6,5,4,7}|.
%    \bigskip
%    
%    \textbf{v1.3a\&b 2000/7/28 \& 2000/7/30}
%    \medskip
%    
%    \emph{Introductions:} (a) It is now possible to force \TeXshade{} to 
%    display gap symbols before and after the actual sequence 
%    by the commands `|\showleadinggaps|' and `|\hideleadinggaps|'
%    (\ref{Lshowleadinggaps}).
%    (b) The sequence names input routine is now more tolerant concerning
%    special characters.
%    \bigskip
%    
%    \textbf{v1.3 2000/3/3}
%    \medskip
%    
%    \emph{Corrections:} Line scrambling occured when features where
%    set in the |ttop| row without a feature in the |top| row. Fixed.
%    The incompatible command `|\language|' with the |babel| package has been
%    replaced by `|\germanlanguage|' and `|\englishlanguage|'\footnote%
%    {Thanks to Eckhart Guth\"ohrlein.}.
%    
%    \emph{Introductions:} (a) Now, translations of sequence stretches
%    are possible. Either nucleotide or amino acid sources can be 
%    translated. This is done by the new |{translate}| option for the 
%    feature command. (b) The codons are defined by the new command
%    `|\codon|'. Complete codon sets can be loaded by `|\geneticcode|'.
%    (c) Further, the size and style of the nucleotide triplets of
%    backtranslations can be set by `|\backtranslabel|' and 
%    `|\backtranstext|'. (d) Two more feature counter styles were introduced:
%    `|\Romancount|' and `|\romancount|'. (e) \TeXshade{} is now 
%    compatible with \TeXtopo, a new \TeX{} software
%    for drawing and shading topology plots of membrane proteins.
%    \bigskip
%    
%    \textbf{v1.2a 1999/6/24 (not released)}
%    \medskip
%    
%    \emph{Minor corrections:} `|\namecolor|' and `|\numbercolor|' are 
%    now really correctly reordered. Brackets ( and ) are now allowed
%    in sequence names. The option |{case}| in `|\funcshadingstyle|' 
%    works now.
%    \bigskip
%    
%    \textbf{v1.2 1999/6/12}
%    \medskip
%    
%    \emph{Corrections:} (a) Functional group definitions of more than
%    seven groups produced an error when displaying group number
%    eight. These residues where skipped in the alignment. Fixed.
%    
%    \emph{Introductions:} (a) Protein secondary structure files in the DSSP,
%    STRIDE and PHD format can be included and displayed auto\-matically
%    within the alignment by `|\includeDSSP|' (and similar commands for 
%    STRIDE, PHDsec and PHDtopo, \ref{structure}).
%    (b) Which types of secondary structures are to be included or
%    skipped in the alignment is chosen by `|\showonDSSP|' and 
%    `|\hideonDSSP|' (and respective commands for STRIDE, PHDsec and PHDtopo).
%    (c) The appearance of the labels is defined by `|\appearance|'.
%    (d) Internal counters for repeatedly occuring structure types
%    can be activated by `|\numcount|', `|\alphacount|' and
%    `|\Alphacount|'. All commands are described in \ref{structure}.
%    \bigskip
%        
%    \textbf{v1.1 1999/5/26}
%    \medskip
%    
%    \emph{Corrections:} (a) The activation of `|emphregion|' lead to 
%    an em\-pha\-sized following alignment. This has been 
%    corrected. (b) `|\namecolor|' and `|\numbercolor|' were not 
%    reordered with the command `|orderseqs|'. Fixed. (c) Sequence 
%    gaps at the beginning or the end of a sequence, i.\,e. before
%    the first and after the last residue where labeled with the
%    gap symbol. Now these positions are left blank.
%    
%    \emph{Introductions:} (a) In order to treat the preceeding and 
%    sequence following gaps correctly, \TeXshade{} needs to know the
%    length of the sequences. Therefore, the command `|\seqlength|' was
%    introduced (\ref{seqlines}). (b) With `|\gapcolors|' (also 
%    \ref{seqlines}) the
%    color selection for gap symbols is independent from non conserved
%    residues. (c) The divisions of the ruler where so far fixed to
%    10. Now, this value is changeable by `|\rulersteps|' (again 
%    \ref{seqlines}). (d) `|\hideresidues|' and `|\showresidues|' turn
%    off or on the residue names, i.\,e. one can choose between a
%    display of shaded boxes only or with letters in the boxes 
%    (\ref{kill}). (e) The changes (c) through (d) were necessary 
%    for the introduction of `|\fingerprint|'. This command allows one to
%    display the complete sequence in one line for an easy survey of
%    the alignment (\ref{fingerprint}).
%    \bigskip
%    
%    \textbf{v1.0 1999/5/12}
%    \medskip
%    
%    First release.
%    \bigskip
%    
%    
%    \subsection{\LaTeX{} basics}
%    
%    \subsubsection{Typesetting documents using \LaTeX}
%    
%    In order to use any of the macros provided by the 
%    \BioTeX-project 
%    (\TeXshade/\TeXtopo) efficiently a basic understanding of the \TeX{} 
%    typesetting system and its usage is required. Several books are
%    available on this topic, but a rather quick and easy introduction
%    is the \emph{Not so short introduction to \LaTeX}. This document
%    is available from all Comprehensive \TeX{} Archive Network 
%    (CTAN) servers,
%    e.\,g. from |ftp://ftp.dante.de/pub/tex/documentation/lshort/|,
%    in many different languages and formats besides \LaTeX{}, such 
%    as \textsc{PostScript} and on-line viewable PDF.
%    I also put a link from the \BioTeX{} (\TeXshade/\TeXtopo) homepage 
%    to the document collection
%    (|http://pharmazie.uni-kiel.de/chem/Prof_Beitz/BioTeX|).
%    
%    
%    \subsubsection{Memory shortness when using \TeX{}shade}
%    
%    If you are using \TeXshade{} to align several large sequences (about 1000
%    residues/sequence), LaTeX will probably stop compiling and quit with one
%    of the following messages: 
%    
%    |!\ TeX capacity exceeded, sorry [main memory size=384000]| 
%    
%    or 
%    
%    |!\ TeX capacity exceeded, sorry [stack size=300]|.
%    
%    \TeX{} allocates space for different kinds of internal variables. 
%    Setting alignments needs lots of memory,
%    usually more than for typesetting plain text.
%    Thus, the parameter settings of a standard \TeX{} installation might not
%    be sufficient for certain projects. This manifests
%    in \TeX{} error messages about insufficient memory  
%    and the setting process is interrupted. There is no reason to be 
%    concerned. The parameters can be set by hand. Unfortunately, 
%    each \TeX{} system hides its default parameter file in a different
%    place in the system. 
%    
%    In the following, an excerpt from the FAQ-list to \TeXshade{} is added. 
%    This explains how 
%    to increase the settings in Oz\TeX{} for the Macintosh, Mik\TeX{} 
%    for Windows and te\TeX{} for *NIX \TeX{} distributions. Please contribute 
%    to this list!
%    
%    \begin{enumerate}
%    
%    \item
%    
%    \textbf{Oz\TeX{} 4.0 for the Macintosh:}
%    
%    Find the file `OzTeX:TeX:Configs:Default'. This file contains
%    all memory settings. Look for the section 
%    `\% TeX parameters' and increase the values that \TeX{} complains
%    about during the run. You will have to restart Oz\TeX{} before the
%    changes are active.
%    
%    For older versions of Oz\TeX{} the configuration file has the 
%    same name but the path is somewhat different.
%    
%    
%    \item
%    
%    \textbf{te\TeX{} for *NIX:} (contributed by Joerg Daehn)
%    
%    Find the file: `/usr/share/texmf/web2c/texmf.cnf' or use 
%    
%    |locate texmf.cnf| at the command prompt to find it.
%
%    Login as super user. Backup `texmf.cnf' in case you destroy something and
%    then open the `texmf.cnf' file in your favorite text editor and use its
%    search function to locate |main_memory|. This variable is set to 384000.
%    Change this to some higher value, i.e. 4000000 (works fine for me!). The
%    total amount of memory should not exceed 8000000, so check the other
%    values in that section. 
%
%    Next, you want to change the stack size. Search for |stack_size|. This
%    will be set to 300. I changed it to 4000 and it works fine.
%
%    There might be complains by \TeX{} about further specific parameters such
%    as |stack_size|. You find all those in the same file.
%
%    After this you have to run `texconfig init'.
%
%    Logout as root.
%
%    After this all should be set for large alignments. Happy \TeX{}ing!
%
%    The information on how to achieve this was derived from a mail in the
%    te\TeX{} mail archive. The original question was posted by Pascal Francq and
%    answered by Rolf Nieprasch.
%
%    
%    \item
%    
%    \textbf{MiK\TeX{} for Windows:}
%    
%    The MiK\TeX{} documentation describes very detailed how the memory
%    settings can be changed. In brief, you must locate the 
%    configuration file `miktex/config/miktex.ini'. In the [MiKTeX] 
%    section of this file you find all the parameters you need, e.\,g.\ 
%    |mem_min|, |mem_max|, |buf_size|, |stack_size| etc.
%    
%    It appears, that the standard settings of MiK\TeX{} are bigger 
%    than that of other \TeX{} installations, so it may not always be necessary 
%    to increase the values.
%    
%    
%    \end{enumerate}
%    
%    
%
%    \subsection{System requirements} \label{require}
%    
%    \TeXshade{} requires \LaTeXe{} with |color.sty| and |graphics.sty|
%    for shading. For arrows in the feature line (p.\pageref{Lfeature})  
%    the AMS Math style is needed.
%    David Carlisle's |color.sty| is part of the Standard \LaTeX{}
%    `Graphics Bundle' [1]. This and the other packages can be downloaded 
%    from any \TeX{} archive, e.g.\ |ftp.dante.de|; usually they are 
%    included in a comprehensive \TeX{} installation. 
%
%    The |color| style allows one to use several |[|\meta{options}|]|, e.\,g.
%    |dvips|, |pdftex| or |dviwin|. These provide the commands which
%    different devices/programs need to display colored output. It is 
%    advisable to make yourself familiar with the |color.sty| manual. 
%    You should define a default driver in the file |color.cfg|.
%    Since there is no direct call of |color.sty| by the user, the 
%    option can be stated when \TeXshade{} is loaded, see next 
%    subsection. If no option is stated the |DVIPS| driver will be 
%    loaded. 
%     
%    With the |[dvips]| option the output DVI-file 
%    can be converted to \textsc{PostScript} using the |DVIPS| program
%    and can later be viewed or printed with the public domain 
%    {\sc GhostView} program which is
%    available for almost all computer platforms. Further, more and more
%    standard \TeX{} viewers are to a certain extent \textsc{PostScript} 
%    compatible. 
%    \bigskip
%    
%    \subsection{The \texttt{texshade} environment}
%    
%    \label{tsenvironment}
%    
%    The commands provided by the \TeXshade{} package are enabled by
%    the following command in the document header section:
%    \medskip
%    
%    \quad |\usepackage[|\meta{option}|]{texshade}|
%    
%    \medskip
%    Make sure that the file `|texshade.sty|' is present in a directory
%    searched by \TeX{} (see the installation notes in the file
%    `|texshade.txt|').
%    
%    The \meta{option} given here is passed to |color.sty| which 
%    handles the color commands for a particular output device, see 
%    previous subsection and the |color.sty| manual.
%    
%    The \TeXshade{} package provides only one single new environment:
%    |texshade|. This environment has one mandatory and
%    one optional argument, both of them designating file names which
%    must be present in a directory searched by \TeX. The
%    required file \meta{alignmentfile} contains the aligned nucleotide 
%    or peptide sequences
%    (see section~\ref{alignfilestruc}). This file is needed, because 
%    \TeXshade{} does no alignment by 
%    itself, it has to take a preprocessed alignment as input.
%    The optional file is a parameter file (section~\ref{paramfilestruc})
%    with definitions for the
%    customized calculation of the consensus, special sequence features
%    or labels etc. In this parameter file all \TeXshade{} commands 
%    which are allowed in the |texshade| environment can be used and are 
%    fully functional.
%    Within the environment further \TeXshade{} commands can be given
%    to replace or complete settings from the parameter file.
%    
%    Thus, setting an alignment with \TeXshade{} is as simple as
%    this:
%    
%    \begin{quote}
%    |\begin{texshade}[|\meta{parameterfile}|]|
%         |{|\meta{alignmentfile}|}|
%         
%    \quad\emph{further \emph{\TeXshade} commands, if needed}
%    
%    |\end{texshade}|
%    \end{quote}
%    
%    \subsection{Shading modes predefined in this package}
%    
%    \subsubsection{Identity mode}
%    
%    \label{ident}
%     
%    This basic type of shading is provided by almost any alignment
%    program. All identical residues at a position are shaded if the
%    number of matching residues is higher than a given threshold
%    (default is 50\%).\medskip
%    
%    \begin{texshade}{AQPpro.MSF}
%       \setends{1}{80..112}
%       \hideconsensus
%    \end{texshade}
%
%    Code:\medskip
%
%    \vbox{%
%    \begin{verbatim}    
%    \begin{texshade}{AQPpro.MSF}
%       \setends{1}{80..112}
%       \hideconsensus
%    \end{texshade}
%    \end{verbatim}  
%    }  
%    
%    If you like, positions where conservation is very high (here $\ge$ 80\%) can
%    be shaded in a special color and the consensus can be shown with
%    or without shading according to the degree of conservation:
%    \medskip\label{shadecons}
%    
%    \begin{texshade}{AQPpro.MSF}
%       \threshold[80]{50}
%       \setends{1}{80..112}
%       \showconsensus[ColdHot]{bottom}
%       \defconsensus{.}{lower}{upper}
%       \showlegend
%    \end{texshade}
%    
%    Code:\medskip
%
%    \vbox{%
%    \begin{verbatim}    
%    \begin{texshade}{AQPpro.MSF}
%       \threshold[80]{50}
%       \setends{1}{80..112}
%       \showconsensus[ColdHot]{bottom}
%       \defconsensus{.}{lower}{upper}
%       \showlegend
%    \end{texshade}
%    \end{verbatim}}
%    
%    \subsubsection{Similarity mode}
%    
%    \label{similar}
%    
%    In many cases it is expedient---mostly when comparing protein
%    sequences---to shade also residues
%    which are not identical but similar to the consensus sequence.
%    Consider a position where three out of five residues are basic
%    arginines and two more residues are also basic but lysines.
%    In similarity mode \TeXshade{} shades similar residues in a different 
%    color to distinguish them from the consensus residue. Even when 
%    none of the residues alone reaches the 
%    threshold but a group of similar residues does these are shaded
%    in the `similarity' color. This case is given for instance
%    when at a position in a five sequence alignment two aliphatic 
%    valines and two also aliphatic isoleucins are present and the 
%    threshold is set to 50\%. Neither residue exceeds this percentage 
%    but as a group of similars they do. 
%    
%    In grayscale printouts some colors of the following alignment may appear 
%    undistinguishable. Don't worry if you usually use grayscale---all 
%    colors/grays can be selected freely (see \ref{colors}).
%    \medskip 
%    
%    \begin{texshade}{AQPpro.MSF}
%       \shadingmode{similar}
%       \threshold[80]{50}
%       \setends{1}{80..112}
%       \hideconsensus
%       \feature{top}{1}{93..93}{fill:$\downarrow$}{first case (see text)}
%       \feature{bottom}{1}{98..98}{fill:$\uparrow$}{second case (see text)}
%    \end{texshade}    
%    
%    Code:\medskip
%
%    \vbox{%
%    \begin{verbatim}    
%    \begin{texshade}{AQPpro.MSF}
%       \shadingmode{similar}
%       \threshold[80]{50}
%       \setends{1}{80..112}
%       \hideconsensus
%       \feature{top}{1}{93..93}{fill:$\downarrow$}{first case (see text)}
%       \feature{bottom}{1}{98..98}{fill:$\uparrow$}{second case (see text)}
%    \end{texshade}    
%    \end{verbatim}}
%    
%    Probably you know 
%    this kind of shading from the public domain program 
%    |BoxShade| 
%    by \textsc{Kay Hofmann} or from the Macintosh version 
%    |MacBoxShade| by \textsc{Michael D. Barron}. \TeXshade{}
%    provides the same functionality---and goes truly beyond---for the 
%    \TeX{} community.
%
%    
%    \subsubsection{T-Coffee shading}
%    
%    \label{TCoffee}
%    
%    \TeXshade{}'s capabilities of calculating alignment shadings are 
%    limited. |T-Coffee| (|www.tcoffee.org|) is a sophisticated alignment/shading 
%    software. You can apply shading from |T-Coffee| in \TeXshade{}
%    by loading the shading information file (|score_ascii|) generated by
%    |T-Coffee|.
%    \medskip 
%    
%
%    \begin{texshade}{AQPpro.MSF}
%       \shadingmode[AQP_TC.asc]{T-Coffee}
%       \setends{1}{30..63}
%       \hideconsensus
%       \feature{top}{1}{30..63}{color:conservation[T-Coffee]}{}
%       \showfeaturestylename{top}{feat-cons}
%       \showconsensus{bottom}
%    \end{texshade}    
%    
%    Code:\medskip
%
%    \vbox{%
%    \begin{verbatim}    
%    \begin{texshade}{AQPpro.MSF}
%       \shadingmode[AQP_TC.asc]{T-Coffee}
%       \setends{1}{30..63}
%       \hideconsensus
%       \feature{top}{1}{30..63}{color:conservation[T-Coffee]}{}
%       \showfeaturestylename{top}{feat-cons}
%       \showconsensus{bottom}
%    \end{texshade}    
%    \end{verbatim}}
%    
%    
%    
%    
%    
%    
%    
%    \subsubsection{Diversity mode}
%    
%    \label{diverse}
%    
%    Contrary to the above described modes this shading style displays
%    sequence differences. Thus, it is most suitable for comparing very
%    similar sequences, e.\,g.\ species variants of a protein.
%    
%    One sequence is used as consensus. 
%    Matching residues in other sequences are blanked out, 
%    mismatches are shown in lowercase.
%    \medskip
%        
%    \begin{texshade}{AQP2spec.ALN}
%       \seqtype{P}
%       \shadingmode{diverse}
%       \setends{1}{77..109} \residuesperline*{33}
%       \featureslarge
%       \feature{top}{1}{77..109}{}{AQP2 species variants}
%       \namesrm\namessl
%       \hidenumbering
%       \showruler{top}{1}
%       \shownames{left}
%       \nameseq{1}{Bos taurus}
%       \nameseq{2}{Canis familiaris}
%       \nameseq{3}{Dugong dugong}
%       \nameseq{4}{Equus caballus}
%       \nameseq{5}{Elephas maximus}
%       \frameblock{1}{82..82,106..106}{Red[1pt]}
%    \end{texshade}\label{frame}
%    
%    Code:\medskip
%
%    \vbox{%
%    \begin{verbatim}    
%    \begin{texshade}{AQP2spec.ALN}
%       \seqtype{P}
%       \shadingmode{diverse}
%       \setends{1}{77..109}
%       \featureslarge
%       \feature{top}{1}{77..109}{}{AQP2 species variants}
%       \namesrm\namessl
%       \hidenumbering\showruler{top}{1}
%       \shownames{left}
%       \nameseq{1}{Bos taurus}
%       \nameseq{2}{Canis familiaris}
%       \nameseq{3}{Dugong dugong}
%       \nameseq{4}{Equus caballus}
%       \nameseq{5}{Elephas maximus}
%       \frameblock{1}{82..82,106..106}{Red[1pt]}
%    \end{texshade}\label{frame}
%    \end{verbatim}}   
%    
%    
%    \subsubsection{Functionality modes}
%    
%    \label{func}
%    
%    Displaying functional peptide similarities is one of \TeXshade's
%    strong capabilities. Six functional shading modes are predefined;
%    further user specific modes can easily be created. The examples 
%    may not look very impressive when printed in grayscale. Enjoy 
%    them on your screen or use color printouts. As mentioned before,
%    all colors can be changed to others or to grays without restrictions
%    (see chapter \ref{colors}).
%    
%    \begin{itemize}
%    \item [\textbf{charge}:] residues which are charged at physiological pH
%                    (7.4) are shaded if their number at a position
%                    is higher than the threshold \label{charge}
%                    
%    \begin{texshade}{AQPpro.MSF}
%       \shadingmode[charge]{functional}
%       \setends{1}{138..170}
%       \feature{top}{3}{153..165}{bar[-50,50]:-50,-45,%
%          -40,-30,-20,-10,0,10,20,30,40,45,50}{}
%       \feature{top}{3}{167..186}{color:5,10,15,20,25,30,35,%
%          40,45,50,55,60,65,70,75,80,85,90,95,100[ColdHot]}{}
%       \showlegend
%    \end{texshade}
%    
%    Code:\medskip
%
%    \vbox{%
%    \begin{verbatim}    
%    \begin{texshade}{AQPpro.MSF}
%       \shadingmode[charge]{functional}
%       \setends{1}{138..170}
%       \feature{top}{3}{153..165}{bar[-50,50]:-50,-45,%
%          -40,-30,-20,-10,0,10,20,30,40,45,50}{}
%       \feature{top}{3}{167..186}{color:5,10,15,20,25,30,35,%
%          40,45,50,55,60,65,70,75,80,85,90,95,100[ColdHot]}{}
%       \showlegend
%    \end{texshade}
%    \end{verbatim}}
%    
%    \item [\textbf{hydropathy}:] discrimination between acidic and
%                        basic, polar uncharged and hydrophobic nonpolar residues
%                        \label{hydro}
%    
%    \begin{texshade}{AQPpro.MSF}
%       \shadingmode[hydropathy]{functional}
%       \feature{top}{1}{158..163}{brace}{tinted}
%       \tintblock{1}{158..163}
%       \setends{1}{138..170}
%       \showlegend
%    \end{texshade}
%    
%    Code:\medskip
%
%    \vbox{%
%    \begin{verbatim}    
%    \begin{texshade}{AQPpro.MSF}
%       \shadingmode[hydropathy]{functional}
%       \feature{top}{1}{158..163}{brace}{tinted}
%       \tintblock{1}{158..163}
%       \setends{1}{138..170}
%       \showlegend
%    \end{texshade}
%    \end{verbatim}}    
%    
%    
%    \item [\textbf{structure}:] displays the potential
%                        localization within the tertiary structure of
%                        the protein \label{struc}
%    
%    \begin{texshade}{AQPpro.MSF}
%       \shadingmode[structure]{functional}
%       \setends{1}{138..170}
%       \feature{top}{1}{138..157}{box[Blue,Red][0.5pt]: %
%           $\alpha$-helix[Yellow]}{transmembrane domain 4}
%       \feature{top}{1}{158..163}{translate[Blue]}{}
%       \backtranslabel{oblique}
%       \feature{bottom}{1}{158..163}{brace[Blue]}{loop D [Blue]}
%       \feature{top}{1}{164..170}{o->[Red]}{trans. dom. 5}
%       \showlegend
%    \end{texshade}
%          
%    Code:\medskip
%
%    \vbox{%
%    \begin{verbatim}    
%    \begin{texshade}{AQPpro.MSF}
%       \shadingmode[structure]{functional}
%       \setends{1}{138..170}
%       \feature{top}{1}{138..157}{box[Blue,Red][0.5pt]: %
%           $\alpha$-helix[Yellow]}{transmembrane domain 4}
%       \feature{top}{1}{158..163}{translate[Blue]}{}
%       \backtranslabel{oblique}
%       \feature{bottom}{1}{158..163}{brace[Blue]}{loop D [Blue]}
%       \feature{top}{1}{164..170}{o->[Red]}{trans. dom. 5}
%       \showlegend
%    \end{texshade}
%    \end{verbatim}}   
%          
%    
%    \item [\textbf{chemical}:] residues are shaded due to chemical 
%                      properties of
%                      their functional groups \label{chem}
%                      
%    \begin{texshade}{AQPpro.MSF}
%       \shadingmode[chemical]{functional}
%       \setends{1}{138..170}
%       \showlegend
%    \end{texshade}
%          
%    Code:\medskip
%
%    \vbox{%
%    \begin{verbatim}    
%    \begin{texshade}{AQPpro.MSF}
%       \shadingmode[chemical]{functional}
%       \setends{1}{138..170}
%       \showlegend
%    \end{texshade}
%    \end{verbatim}}    
%          
%          With |\shadeallresidues| the threshold is ignored and
%          all residues are shaded due to their group assignment.
%          This is \emph{not} identical to a threshold of 0\%
%          where only the majority group would be shaded. See the
%          difference:
%          
%    \begin{texshade}{AQPpro.MSF}
%       \shadingmode[chemical]{functional}
%       \setends{1}{138..170}
%       \shadeallresidues
%    \end{texshade}
%          
%    Code:\medskip
%
%    \vbox{%
%    \begin{verbatim}    
%    \begin{texshade}{AQPpro.MSF}
%       \shadingmode[chemical]{functional}
%       \setends{1}{138..170}
%       \shadeallresidues
%    \end{texshade}
%    \end{verbatim}}    
%          
%    
%    \item [\textbf{rasmol}:] similar to |[chemical]| but with
%                      shading following the rasmol
%                      color scheme \label{ras}
%    \bigskip
%                      
%    \bigskip
%                      
%    \begin{texshade}{AQPpro.MSF}
%       \shadingmode[rasmol]{functional}
%       \setends{1}{138..170}
%       \showruler{top}{1}
%       \rulersteps{1}
%       \namerulerpos{150}{site A[Red]}
%       \namerulerpos{155}{site B[Green]}
%       \shadeallresidues
%       \showlegend
%    \end{texshade}
%          
%    Code:\medskip
%
%    \vbox{%
%    \begin{verbatim}    
%    \begin{texshade}{AQPpro.MSF}
%       \shadingmode[rasmol]{functional}
%       \setends{1}{138..170}
%       \showruler{bottom}{1}
%       \rulersteps{1}
%       \namerulerpos{150}{site A[Red]}
%       \namerulerpos{155}{site B[Green]}
%       \shadeallresidues
%       \showlegend
%    \end{texshade}
%    \end{verbatim}}    
%          
%          
%          
%    \item [\textbf{standard area}:] this shading displays the 
%                      differences in the surface 
%                      area \label{starea}
%                      of the different amino acid's sidechains
%                      
%    \begin{texshade}{AQPpro.MSF}
%       \shadingmode[standard area]{functional}
%       \setends{1}{138..170}
%       \showlegend
%       \shadeallresidues
%    \end{texshade}
%          
%    Code:\medskip
%
%    \vbox{%
%    \begin{verbatim}    
%    \begin{texshade}{AQPpro.MSF}
%       \shadingmode[standard area]{functional}
%       \setends{1}{138..170}
%       \showlegend
%       \shadeallresidues
%    \end{texshade}
%    \end{verbatim}}    
%          
%    \item [\textbf{accessible area}:] \label{accarea} 
%                     here, the surface area which can
%                     be accessed by solvent molecules is used as a 
%                     basis for shading; low accessibility means 
%                     hydrophobic (i.\,e.\ strongly buried 
%                     residues), whereas highly accessible 
%                     sidechains are hydrophilic (compare to
%                     \textbf{hydropathy} and \textbf{structure})
%                   
%    \begin{texshade}{AQPpro.MSF}
%       \shadingmode[accessible area]{functional}
%       \setends{1}{138..170}
%       \showlegend
%       \feature{top}{1}{138..157,164..170}{helix}{membr.}
%       \feature{top}{1}{158..163}{---}{loop}
%       \featurerule{1mm}
%       \shadeallresidues
%    \end{texshade}
%
%    Code:\medskip
%
%    \vbox{%
%    \begin{verbatim}    
%    \begin{texshade}{AQPpro.MSF}
%       \shadingmode[accessible area]{functional}
%       \setends{1}{138..170}
%       \showlegend
%       \feature{top}{1}{138..157,164..170}{helix}{membr.}
%       \feature{top}{1}{158..163}{---}{loop}
%       \featurerule{1mm}
%       \shadeallresidues
%    \end{texshade}
%    \end{verbatim}}    
%
%    \end{itemize}
%    
%    
%    
%    \subsection{Bar graphs and color scales}
%    
%   \label{graphs}
%    
%    Amino acid properties, such as hydrophobicity, molecular weight,
%    or charge can be shown as bar graphs or color scales along the
%    alignment. Further, the degree of protein sequence conservation 
%    can be indicated. As an example, in the following  
%    aquaporin alignment plots of residue conservation (bars, top), 
%    are shown as well as properties of the AQP1 sequence: charge (scale, top), 
%    molecular weight are shown (scale, bottom), and hydrophobicity (bars, bottom).
%    
%    
%    \begin{texshade}{AQPpro.MSF}
%       \setends{1}{138..170}
%       \feature{ttop}{1}{138..170}{bar:conservation}{}
%       \showfeaturestylename{ttop}{conserv.}
%       \ttopspace{-\baselineskip}
%       \feature{top}{1}{138..170}{color:charge}{}
%       \showfeaturestylename{top}{charge}
%       \feature{bottom}{1}{138..170}{color:molweight[ColdHot]}{}
%       \showfeaturestylename{bottom}{weight}
%       \bbottomspace{-\baselineskip}
%       \feature{bbottom}{1}{138..170}{bar:hydrophobicity[Red,Gray10]}{}
%       \showfeaturestylename{bbottom}{hydrophob.}
%       \featurestylenamescolor{Red}
%       \featurestylenamesrm
%       \featurestylenamesit
%       \hideconsensus
%    \end{texshade}
%          
%    Code:\medskip
%
%    \vbox{%
%    \begin{verbatim}    
%    \begin{texshade}{AQPpro.MSF}
%       \setends{1}{138..170}
%       \feature{ttop}{1}{138..170}{bar:conservation}{}
%       \showfeaturestylename{ttop}{conserv.}
%       \ttopspace{-\baselineskip}
%       \feature{top}{1}{138..170}{color:charge}{}
%       \showfeaturestylename{top}{charge}
%       \feature{bottom}{1}{138..170}{color:molweight[ColdHot]}{}
%       \showfeaturestylename{bottom}{weight}
%       \bbottomspace{-\baselineskip}
%       \feature{bbottom}{1}{138..170}{bar:hydrophobicity[Red,Gray10]}{}
%       \showfeaturestylename{bbottom}{hydrophob.}
%       \featurestylenamescolor{Red}
%       \featurestylenamesrm
%       \featurestylenamesit
%       \hideconsensus
%    \end{texshade}
%    \end{verbatim}}    
%          
%    
%    
%    \subsection{Secondary structures}
%    
%   \label{sec}
%    
%    Predicted protein secondary structures in the DSSP, STRIDE
%    PHD or HMMTOP file format can be included and displayed in the
%    alignment. As an example, the following few commands show an 
%    aquaporin alignment with the PHD topology data for aquaporin 
%    type 1 (top sequence).
%    
%    \vbox{%
%          \begin{verbatim}
%          \begin{texshade}{AQPpro.MSF}
%             \shadingmode[allmatchspecial]{similar}
%             \includePHDtopo{1}{AQP1.phd}
%          \end{texshade}
%          \end{verbatim}
%    }         
%    
%    Abbr.: \emph{int.} -- internal; \emph{ext.} -- external; \emph{TM} --
%    transmembrane domain
%    
%          \begin{texshade}{AQPpro.MSF}
%             \shadingmode[allmatchspecial]{similar}
%             \includePHDtopo{1}{AQP1.phd}
%          \end{texshade}
%    
%    \subsection{Sequence fingerprints}
%    
%    \label{finger}
%    
%    To gain a quick overview of sequence similarities or properties 
%    the |\fingerprint| command has been implemented. It can depict the 
%    complete sequence in one single line. The residues are presented 
%    as colored vertical lines. The implementation of this kind of output
%    was inspired by a publication by \textsc{Kai-Uwe Fr\"ohlich} [6].
%    \medskip
%    
%    \begin{texshade}{AQPpro.MSF}
%       \shadingmode[allmatchspecial]{similar}
%       \shadingcolors{grays}
%       \fingerprint{360}
%       \showlegend
%       \feature{top}{1}{13..36,51..68,94..112,138..156,%
%                        165..185,211..232}{,-,}{TM}
%    \end{texshade}
%    
%    Code:\medskip
%
%    \vbox{%
%    \begin{verbatim}    
%    \begin{texshade}{AQPpro.MSF}
%       \shadingmode[allmatchspecial]{similar}
%       \shadingcolors{grays}
%       \fingerprint{360}
%       \showlegend
%       \feature{top}{1}{13..36,51..68,94..112,138..156,%
%                        165..185,211..232}{,-,}{TM}
%    \end{texshade}
%    \end{verbatim}}    
%    
%    The higher the similarity the darker the vertical lines. In this 
%    overview it becomes obvious that the transmembrane regions of the 
%    aquaporin isoforms are most conserved.
%    \medskip
%    
%    A fingerprint of charge distribution on different aquaporins is shown. 
%    below. Sequence gaps can be left blank (example above) or drawn as lines
%    between the sequence blocks.
%    
%    \begin{texshade}{AQPpro.MSF}
%       \shadingmode[charge]{functional}
%       \shadeallresidues
%       \fingerprint{360}
%       \gapchar{rule}
%       \showlegend
%    \end{texshade}
%
%
%    Code:\medskip
%
%    \vbox{%
%    \begin{verbatim}    
%    \begin{texshade}{AQPpro.MSF}
%       \shadingmode[charge]{functional}
%       \shadeallresidues
%       \fingerprint{360}
%       \gapchar{rule}
%       \showlegend
%    \end{texshade}
%    \end{verbatim}}    
%
%    
%    \subsection{Sequence logos}
%    
%    \label{logo}
%    
%    Sequence logos represent the information content of the aligned 
%    sequences at a position in bit (max.\ 2 bit for DNA, i.\,e.
%    log$_2$4, and 4.322 bit for proteins, i.\,e. log$_2$20) and the 
%    relative frequency of a base or amino acid at this 
%    position [7]. Thus, more information is contained in logos than in
%    a standard consensus sequence.
%    The example below shows a DNA sequence alignment with the logo on the  
%    top.
%
%    It must be remarked that a logo from only five sequences does not
%    produce meaningful results - it rather illustrates the technique.
%
%    \medskip
%    
%    \begin{texshade}{AQPDNA.MSF}
%       \setends{1}{414..443}
%       \showsequencelogo{top}
%    \end{texshade}
%    
%    Code:\medskip
%
%    \vbox{%
%    \begin{verbatim}    
%    \begin{texshade}{AQPDNA.MSF}
%       \setends{1}{414..443}
%       \showsequencelogo{top}
%    \end{texshade}
%    \end{verbatim}}    
%    
%    
%    Next, only the logo of a protein alignment is displayed plus the 
%    degree of sequence conservation as a color scale in the consensus 
%    line. Note, that the full functionality of the feature lines remains.
%    \medskip
%    
%    \begin{texshade}{AQPpro.MSF}
%       \setends{AQP3.PRO}{203..235}
%       \showsequencelogo{top} \showlogoscale{leftright}
%       \hideseqs
%       \residuesperline*{33}
%       \defconsensus{{$\bullet$}}{{$\bullet$}}{{$\bullet$}}
%       \showconsensus[ColdHot]{bottom}
%       \nameconsensus{conservation} \namessf\namessl
%       \showruler{bottom}{AQP3.PRO} \rulersteps{1}
%       \feature{top}{AQP3.PRO}{208..210}{---}{NPA}
%       \feature{top}{AQP3.PRO}{211..219}{helix}{}
%       \feature{top}{AQP3.PRO}{220..232}{brace}{loop E}
%       \feature{top}{AQP3.PRO}{233..235}{helix}{TM6}
%       \feature{bottom}{AQP3.PRO}{203..235}{brace}{1-step numbering}
%    \end{texshade}
%    
%    Code:\medskip
%
%    \vbox{%
%    \begin{verbatim}    
%    \begin{texshade}{AQPpro.MSF}
%       \setends{AQP3.PRO}{203..235}
%       \showsequencelogo{top} \showlogoscale{leftright}
%       \hideseqs
%       \residuesperline*{33}
%       \defconsensus{{$\bullet$}}{{$\bullet$}}{{$\bullet$}}
%       \showconsensus[ColdHot]{bottom}
%       \nameconsensus{conservation} \namessf\namessl
%       \showruler{bottom}{AQP3.PRO} \rulersteps{1}
%       \feature{top}{AQP3.PRO}{208..210}{---}{NPA}
%       \feature{top}{AQP3.PRO}{211..219}{helix}{}
%       \feature{top}{AQP3.PRO}{220..232}{brace}{loop E}
%       \feature{top}{AQP3.PRO}{233..235}{helix}{TM6}
%       \feature{bottom}{AQP3.PRO}{203..235}{brace}{1-step numbering}
%    \end{texshade}
%    \end{verbatim}} 
%    
%    The same logo is shown below but with frequence correction turned
%    on (|\dofrequencycorrection|), see p.\pageref{Lshowsequencelogo}.
%    This takes into account the difference between the amino acid 
%    distribution in the alignment and the equal distribution of
%    5\% for each residue.
%    \medskip
%
%    \begin{texshade}{AQPpro.MSF}
%       \setends{AQP3.PRO}{203..235}
%       \showsequencelogo{top} \showlogoscale{leftright}
%       \hideseqs
%       \residuesperline*{33}
%       \defconsensus{{$\bullet$}}{{$\bullet$}}{{$\bullet$}}
%       \showconsensus[ColdHot]{bottom}
%       \nameconsensus{conservation} \namessf\namessl
%       \showruler{bottom}{AQP3.PRO} \rulersteps{1}
%       \feature{top}{AQP3.PRO}{208..210}{---}{NPA}
%       \feature{top}{AQP3.PRO}{211..219}{helix}{}
%       \feature{top}{AQP3.PRO}{220..232}{brace}{loop E}
%       \feature{top}{AQP3.PRO}{233..235}{helix}{TM6}
%       \feature{bottom}{AQP3.PRO}{203..235}{brace}{1-step numbering}
%       \dofrequencycorrection
%    \end{texshade}
%    
%
%    \subsection{Subfamily logos}
%    
%    \label{sublogo}
%    
%    The following output is derived from the calculation of a
%    subfamily logo [14]. Such logos display relevant deviations of a
%    subfamily compared to the remaining set of sequences. Here,
%    typical residues of AQP3 are shown (upright) which deviate 
%    from the remaining  four aquaporins of this alignment (upside-down).
%    The output can be directly compared to the sequence logo above,
%    which displays the same section of the alignment. 
%    Note, that five sequences are far too few to obtain meaningful
%    results with this method. This is just to illustrate the 
%    approach.
%    \medskip
%
%    \begin{texshade}{AQPpro.MSF}
%       \setends{AQP3.PRO}{203..235}
%       \residuesperline*{33}
%       \setsubfamily{3} 
%       \showsubfamilylogo{top} \showlogoscale{leftright}
%       \namesubfamilylogo[others]{AQP3}
%       \namessf \namessl
%       \showruler{bottom}{AQP3.PRO} \rulersteps{1}
%       \hideseqs
%       \hideconsensus
%       \dofrequencycorrection
%    \end{texshade}
%
%    Code:\medskip
%
%    \vbox{%
%    \begin{verbatim}    
%    \begin{texshade}{AQPpro.MSF}
%       \setends{AQP3.PRO}{203..235}
%       \residuesperline*{33}
%       \setsubfamily{3} 
%       \showsubfamilylogo{top} \showlogoscale{leftright}
%       \namesubfamilylogo[others]{AQP3}
%       \namessf \namessl
%       \showruler{bottom}{AQP3.PRO} \rulersteps{1}
%       \hideseqs
%       \hideconsensus
%       \dofrequencycorrection
%    \end{texshade}
%    \end{verbatim}} 
%    
%
%
%
%    \subsection{Customization of the alignment output}
%    
%    Extensive possibilities are given to the user to customize 
%    the final output of an alignment. Thus, all parameters defining the
%    appearance of letters can be changed individually for sequence 
%    residues, names and numbering or the describing feature texts. 
%    Additional manual shading can be applied to any region or
%    block of residues. Sequences are easily re-ordered, separated, hidden 
%    or blanked out without recalculation of the entire alignment; 
%    sections of the alignment can also be shown. 
%    Numbering and rulers can be displayed and set to any value. 
%    A powerful tool is the |\feature|
%    command which allows one to label stretches of residues with bars, 
%    arrows, braces or any fill character and describing text. 
%    Legends are set automatically if desired, but user commands
%    are also provided to build individual legends.
%    
%    
%    \newpage
%    \section{Format of alignment input files}
%    
%    \label{alignfilestruc}
%    
%    \TeXshade{} can handle two common alignment input formats, i.\,e.\
%    the MSF format (\underline{m}ultiple \underline{s}equence 
%    \underline{f}ormat) and the ALN format 
%    (\underline{al}ig\underline{n}ment format). The MSF 
%    format is used by |PILEUP| of the Unix GCG sequence
%    analysis package\footnote{For a description see
%    |http://gene.md.huji.ac.il/Computer/GCG9doc|}. Files in the
%    ALN format are produced by |CLUSTAL| which is 
%    available for free for Unix, DOS and Macintosh. Further, upon 
%    request, the FASTA format is supported since version 1.6.
%    In addition to the mentioned software many alignment programs have 
%    export filters for the MSF, ALN or FASTA
%    format, e.\,g.\ |MACAW| produces ALN files. If
%    you are not sure whether your favorite sequence aligner 
%    produces one of the required formats compare its output to
%    the following examples. \TeXshade{} determines the format from
%    the internal file structure, thus extensions like MSF, ALN
%    or FASTA
%    are not required. If you can choose the alignment format 
%    MSF is recommended, because this format gives information
%    about the sequence type, i.\,e.\ peptide or nucleotide sequences, 
%    and length (for the correct setting of gaps at the sequence end).
%    
%    \subsection{The MSF file format}
%    Files of this type are divided into a header section and the 
%    multiple sequence alignment. The header may contain the
%    following components:
%    
%    
%    \begin{itemize}
%    \item[\textbf{File Type}:] (optional) The first header line 
%              reads for nucleic acids alignments
%              |!!NA_MULTIPLE_ALIGNMENT 1.0| and for amino acid sequences
%              |!!AA_MULTIPLE_ALIGNMENT 1.0| (all uppercase).
%    \item[\textbf{Description}:] (optional) Informative text
%              describing what is in the file.
%    \item[\textbf{Dividing line}:] (required!) Must include the 
%              following attributes:
%       \begin{itemize}
%          \item[|MSF|:] Displays the number of bases or residues in 
%                        the multiple sequence alignment.
%          \item[|Type|:] Displays the sequence type, `P' for a peptide
%                         and `N' for a nucleotide alignment.
%          \item[|Checksum|:] Displays an integer value that 
%                        characterizes the contents of the file.
%          \item[|..|] The two periods act as a divider between the 
%                        descriptive information and the following
%                        sequence information.
%       \end{itemize}
%    \item[\textbf{Name/Weight}:] (required!) Must include the name of
%             each sequence included in the alignment, as well as its
%             length, checksum and weight.
%    \item[\textbf{Two slashes} (|//|):] (required!) This separating 
%             line divides the name/weight information from the 
%             sequence alignment
%    \end{itemize}
%    
%    The alignment section consists of sequence blocks divided by an
%    empty line. Each sequence line starts out with the sequence name.
%    An example file is shown here:
%    \medskip
%    
%    \parindent-1mm
%    \begin{fmpage}
%    \begin{verbatim}
%    
%    AQP.MSF  MSF: 87  Type: P  May 1st, 1998 Check: 2586 ..
%    Name: AQP1.PRO  Len: 66  Check:  1367    Weight: 1.00
%    Name: AQP2.PRO  Len: 58  Check:  2176    Weight: 1.00
%    Name: AQP3.PRO  Len: 83  Check:  1893    Weight: 1.00
%    Name: AQP4.PRO  Len: 63  Check:  3737    Weight: 1.00
%    Name: AQP5.PRO  Len: 59  Check:  3413    Weight: 1.00
%    //
%              1                                           45
%    AQP1.PRO  MAS........................EIKKKLFWRAVVAEFLAM
%    AQP2.PRO  MW.........................ELRSIAFSRAVLAEFLAT
%    AQP3.PRO  M.........NRCG.....EMLHIRYR......LLRQALAECLGT
%    AQP4.PRO  MSDGAAARRWGKCGPPCSRESIMVAFKGVWTQAFWKAVTAEFLAM
%    AQP5.PRO  MK........................KEVCSLAFFKAVFAEFLAT
%    
%              45                                       87
%    AQP1.PRO  TLFVFISIGSALGFNYPLERNQTLVQDNVKVSLAFGLSIATL
%    AQP2.PRO  LLFVFFGLGSALQWA...SS....PPSVLQIAVAFGLGIGIL
%    AQP3.PRO  LILVMFGCGSVAQVVLSRGTHGGF....LTINLAFGFAVTLA
%    AQP4.PRO  LIFVLLSVGSTINWG...GSENPLPVDMVLISLCFGLSIATM
%    AQP5.PRO  LIFVFFGLGSALKWP...SA....LPTILQISIAFGLAIGTL
%    \end{verbatim}
%    \end{fmpage}
%    \bigskip
%    
%    \parindent0mm
%    \TeXshade{} extracts only the information from the file it
%    really needs. So, do not mind all the checksums listed
%    in the file---\TeXshade{} does not either. The same is true 
%    for |Weight|. Required are the string |MSF:| 
%    for the identification of the file format and |Type:| for the 
%    determination of the sequence type (both in the dividing line), 
%    further all |Name:| definitions and finally |//|. The MSF format 
%    allows one to comment out sequences. This is done 
%    by putting an exclamation point directly infront of the respective 
%    |Name|. These sequences are neither displayed nor used for the 
%    calculation of the consensus. This works for \TeXshade, too.
%    To comment out sequences without changing
%    the input file use the \TeXshade{} command 
%    |\killseq{|\meta{seqref}|}| (\ref{kill}). 
%    \medskip
%    
%    \parindent-1mm
%    \begin{fmpage}\label{commout}
%    \begin{verbatim}
%    
%    AQP.MSF  MSF: 87  Type: P  May 1st, 1998 Check: 2586 ..
%    Name: AQP1.PRO  Len: 66  Check:  1367    Weight: 1.00
%    !Name: AQP2.PRO  Len: 58  Check:  2176    Weight: 1.00
%    !Name: AQP3.PRO  Len: 83  Check:  1893    Weight: 1.00
%    Name: AQP4.PRO  Len: 63  Check:  3737    Weight: 1.00
%    Name: AQP5.PRO  Len: 59  Check:  3413    Weight: 1.00
%    //    
%              1                                           45
%    AQP1.PRO  MAS........................EIKKKLFWRAVVAEFLAM
%    AQP2.PRO  MW.........................ELRSIAFSRAVLAEFLAT
%    AQP3.PRO  M.........NRCG.....EMLHIRYR......LLRQALAECLGT
%    AQP4.PRO  MSDGAAARRWGKCGPPCSRESIMVAFKGVWTQAFWKAVTAEFLAM
%    AQP5.PRO  MK........................KEVCSLAFFKAVFAEFLAT
%    
%              45                                       87
%    AQP1.PRO  TLFVFISIGSALGFNYPLERNQTLVQDNVKVSLAFGLSIATL
%    AQP2.PRO  LLFVFFGLGSALQWA...SS....PPSVLQIAVAFGLGIGIL
%    AQP3.PRO  LILVMFGCGSVAQVVLSRGTHGGF....LTINLAFGFAVTLA
%    AQP4.PRO  LIFVLLSVGSTINWG...GSENPLPVDMVLISLCFGLSIATM
%    AQP5.PRO  LIFVFFGLGSALKWP...SA....LPTILQISIAFGLAIGTL
%    \end{verbatim}
%    \end{fmpage}
%    \parindent0mm
%    \bigskip
%    
%    The sequence lengths given after |Len:| are not used by 
%    \TeXshade. Due to the fact that most alignment programms calculate the 
%    sequence length by summing up residues and additionally gaps which 
%    is not really correct. In order to have the sequence break right 
%    after the last residue without printing further gap symbols 
%    \TeXshade{} counts the number of residues by itself. You can  
%    also use the command |\seqlength| in the \TeXshade{}
%    environment to set the values manually if you do not trust a machine.
%    
%    \subsection{The ALN file format}
%    ALN files are quite similar to the above described MSF files.
%    They simply lack a defined header section. Nevertheless, 
%    describing text is allowed before the alignment part. \TeXshade{}
%    determines the number of sequences and their names from the last
%    sequence block---so, no further text lines are allowed after this block!
%    Due to a lacking declaration in the file the sequence type has 
%    to be set in the |texshade| environment by |\seqtype{|\meta{type}|}|
%    \label{Lseqtype} with `P' for peptide and `N' for nucleotide sequences;
%    for the example below: |\seqtype{P}|. If no |\seqtype| command
%    is used \TeXshade{} assumes a nucleotide sequence.
%    \bigskip
%    
%    \parindent-1mm
%    \begin{fmpage}
%    \begin{verbatim}
%    
%                  profalign  May 1st, 1998, 16:58
%                  
%    of AQPpro.MSF{}
%    
%    Muliple alignment parameter:
%    
%    Gap Penalty (fixed):           10.00
%    Gap Penalty (varying):         .05
%    Gap separation penalty range:  8
%    Percent. identity for delay:   0%
%    List of hydrophilic residue:   GPSNDQEKRH
%    Protein Weight Matrix:         blosom
%    
%                      10        20        30        40
%                       .         .         .         .
%    AQP1.PRO  MAS........................EIKKKLFWRAVVAEFLAM
%    AQP2.PRO  MW.........................ELRSIAFSRAVLAEFLAT
%    AQP3.PRO  M.........NRCG.....EMLHIRYR......LLRQALAECLGT
%    AQP4.PRO  MSDGAAARRWGKCGPPCSRESIMVAFKGVWTQAFWKAVTAEFLAM
%    AQP5.PRO  MK........................KEVCSLAFFKAVFAEFLAT
%              *                                  .   ** *.
%    
%    AQP1.PRO  TLFVFISIGSALGFNYPLERNQTLVQDNVKVSLAFGLSIATL
%    AQP2.PRO  LLFVFFGLGSALQWA...SS....PPSVLQIAVAFGLGIGIL
%    AQP3.PRO  LILVMFGCGSVAQVVLSRGTHGGF....LTINLAFGFAVTLA
%    AQP4.PRO  LIFVLLSVGSTINWG...GSENPLPVDMVLISLCFGLSIATM
%    AQP5.PRO  LIFVFFGLGSALKWP...SA....LPTILQISIAFGLAIGTL
%              .. *   .**                    .   **  .
%    \end{verbatim}
%    \end{fmpage}
%    \bigskip
%    
%    The minimal contents of an ALN file are shown below; this 
%    is fully sufficient. Many sequence alignment programs can
%    produce such an output. Have a look at |seqpup| by 
%    \textsc{Don Gilbert} if you need a comprehensive conversion
%    program\footnote{Sorry, |seqpup| is much more!}.
%    \bigskip 
%   
%    \parindent-1mm
%    \begin{fmpage}
%    \begin{verbatim}
%    
%    AQP1.PRO  MAS........................EIKKKLFWRAVVAEFLAM
%    AQP2.PRO  MW.........................ELRSIAFSRAVLAEFLAT
%    AQP3.PRO  M.........NRCG.....EMLHIRYR......LLRQALAECLGT
%    AQP4.PRO  MSDGAAARRWGKCGPPCSRESIMVAFKGVWTQAFWKAVTAEFLAM
%    AQP5.PRO  MK........................KEVCSLAFFKAVFAEFLAT
%    
%    AQP1.PRO  TLFVFISIGSALGFNYPLERNQTLVQDNVKVSLAFGLSIATL
%    AQP2.PRO  LLFVFFGLGSALQWA...SS....PPSVLQIAVAFGLGIGIL
%    AQP3.PRO  LILVMFGCGSVAQVVLSRGTHGGF....LTINLAFGFAVTLA
%    AQP4.PRO  LIFVLLSVGSTINWG...GSENPLPVDMVLISLCFGLSIATM
%    AQP5.PRO  LIFVFFGLGSALKWP...SA....LPTILQISIAFGLAIGTL
%    \end{verbatim}
%    \end{fmpage}
%    \bigskip
%    
%    \subsection{The FASTA file format}
%    In FASTA files each sequence is led
%    by a single description line starting with a `|>|'. \TeXshade{} uses
%    the first word delimited by the leading `|>|' and a space as 
%    the sequence name. If no descriptive text is present \TeXshade{}
%    generates a sequence name consisting of `|seq|' plus a consecutive
%    number. The lines following the description line 
%    contain the sequence.
%    \bigskip
%    
%    \begin{fmpage}
%    \begin{verbatim}
%    
%    >AQP1.PRO  
%    MAS........................EIKKKLFWRAVVAEFLAM
%    TLFVFISIGSALGFNYPLERNQTLVQDNVKVSLAFGLSIATL
%    
%    >AQP2.PRO  
%    MW.........................ELRSIAFSRAVLAEFLAT
%    LLFVFFGLGSALQWA...SS....PPSVLQIAVAFGLGIGIL
%    
%    >AQP3.PRO  
%    M.........NRCG.....EMLHIRYR......LLRQALAECLGT
%    LILVMFGCGSVAQVVLSRGTHGGF....LTINLAFGFAVTLA
%    
%    >AQP4.PRO  
%    MSDGAAARRWGKCGPPCSRESIMVAFKGVWTQAFWKAVTAEFLAM
%    LIFVLLSVGSTINWG...GSENPLPVDMVLISLCFGLSIATM
%    
%    >AQP5.PRO  
%    MK........................KEVCSLAFFKAVFAEFLAT
%    LIFVFFGLGSALKWP...SA....LPTILQISIAFGLAIGTL
%    \end{verbatim}
%    \end{fmpage}
%    \bigskip
%    
%    
%    \parindent0mm
%    \newpage
%    \section{Use of a \TeX{}shade parameter file}
%    
%    \label{paramfilestruc}
%    
%    Using predefined parameter files for repeatedly occuring situations
%    can save a lot of typing and makes the output throughout the 
%    publication or presentation more consistent. Further, such
%    files are an easy way to exchange self-defined shading 
%    modes or new color schemes (i.\,e.\ for a satisfying grayscale output) 
%    with other users. If you have created a
%    parameter file, which you think is of interest for others, please 
%    submit it to me\footnote{|ebeitz@pharmazie.uni-kiel.de|} as an e-mail 
%    attachment together with a short 
%    description. I will take care of those files and post them---with 
%    a reference to the author---together with the next \TeXshade{} 
%    distribution to make them available for all interested users.
%    
%    No special file format is required for parameter 
%    files. \TeXshade{} simply calls the file using the |\input|
%    command right after resetting all parameters to default. An
%    example parameter file is present containing the standard
%    parameters of \TeXshade{} called |texshade.def|. This file can be
%    changed freely and can be used as a template for the creation of
%    personal parameter files. 
%    
%    Five steps are executed by \TeXshade{} when 
%    processing the |texshade| environment:
%    
%    \bigskip
%    \begin{minipage}{12cm}
%    |\begin{texshade}[|\meta{parameterfile}|]{|\meta{alignmentfile}|}|
%    
%    \begin{enumerate}
%    \item Analysis of the \meta{alignmentfile}; determination of 
%    the number of sequences and sequence names
%    
%    \item Setting parameters to default
%    
%    \item Setting parameters to the definitions of the 
%    \meta{parameterfile}, if existent
%    
%    \item Execution of further \TeXshade{} commands within the
%    evironment, if existent
%    
%    \parindent-1cm
%    \medskip
%    |\end{texshade}|
%    
%    \parindent0cm
%    \item Loading and setting the alignment on a line by line basis
%    \end{enumerate}
%    \end{minipage}
%    
%    \newpage
%    \section{\texttt{texshade} user commands}
%    
%    The \TeXshade{} package must be loaded by the |\usepackage|
%    command in the document header section.
%    \medskip
%    
%    \quad|\usepackage[|\meta{option}|]{texshade}|
%    \medskip
%    
%    Then, the |texshade| environment is ready to use as described
%    in \ref{tsenvironment}. See also section \ref{paramfilestruc} for
%    a description of the optional parameter file. All other 
%    commands provided by \TeXshade{} (except |\molweight|, 
%    |\charge| [\ref{molcharge}] and |\shadebox| [\ref{Lshadebox}]) must 
%    be used within the |texshade| environment.
%    
%    
%    
%    \subsection{Using predefined shading modes}
%    
%    \label{predef}
%    
%    \label{Lshadingmode}
%    If no |\shadingmode| command is given in the |texshade| 
%    environment the default shading mode (\emph{identical}, see 
%    \ref{ident}) is active. For the selection of one of the other
%    predefined shading modes the following command is provided.
%    \bigskip
%    
%    \quad |\shadingmode[|\meta{option}|]{|\meta{mode}|}|
%    \bigskip
%    
%    You can choose from four shading modes and declare one option 
%    which depends on the selected mode. 
%    
%    \begin{enumerate}
%    
%    \item |\shadingmode[|\meta{allmatchspecial/number}|]{identical}|
%    
%       There is not much to explain here (see \ref{ident}). Use the
%       option |allmatchspecial| to shade positions with a special color
%       where all residues are identical. Or use a percentage number
%       (0--100) as an option to set an additional threshold for highly
%       conserved residues, e.\,g.\ |\shadingmode[90]{identical}|. 
%       \label{Lallmatchspecial}|\allmatchspecial| can also be 
%       used as a command with or without an optional parameter for
%       setting the high conservation threshold. As both, option or command 
%       |allmatchspecial| is only active in the \emph{identical} and
%       \emph{similar} shading modes.
%       
%       \label{Lshadingcolors}
%       One can choose from five predefined shading color schemes with
%       the command 
%       |\shadingcolors{|\meta{scheme}|}|. The sets are named `blues' 
%       (used in the example, \ref{ident}), `reds', `greens', 
%       `grays' and `black'. Default is |\shadingcolors{blues}|. Further, the colors 
%       for the non matching, the 
%       conserved and all matching (or highly conserved) residues can be set individually 
%       plus the letter case (lower or upper) or any character
%       can be chosen: \label{Lnomatchresidues}
%       \label{Lconservedresidues}
%       \label{Lallmatchresidues} 
%       \bigskip
%       
%       |\nomatchresidues{|\meta{res.col.}|}{|\meta{shad.col.}|}{|\meta{case}|}{|\meta{style}|}|
%       
%       |\conservedresidues{|\meta{res.col.}|}{|\meta{shad.col.}|}{|\meta{case}|}{|\meta{style}|}|
%       
%       |\allmatchresidues{|\meta{res.col.}|}{|\meta{shad.col.}|}{|\meta{case}|}{|\meta{style}|}|
%       \bigskip
%       
%       For how to handle colors for the foreground \meta{res.col.} and 
%       the background \meta{shad.col.} see section \ref{colors}. 
%       The third parameter \meta{case} tells \TeXshade{} to print the
%       corresponding residue as a lowercase or an uppercase letter or
%       even to print any other character. Finally, the \meta{style} 
%       parameter tells \TeXshade{} which shape to use for the letters.
%       Use one of the following styles 
%       for \meta{style}.
%    
%       \begin{center}
%       \begin{tabular}{cl}
%       \meta{style} & \emph{effect} \\ \hline
%       |bf| & bold face series\\
%       |md| & normal series \\
%       |up| & upright shape (normal shape)\\
%       |it| & italics shape \\
%       |sl| & slanted shape \\
%       |rm| & modern roman family \\
%       |sf| & sans serif family \\
%       |tt| & typewriter family \\
%       \end{tabular}
%       \end{center}
%       \medskip    
%    
%       In order to change only some
%       of the parameters it is sufficient to declare these
%       and use empty braces for the others. Examples:
%       \bigskip
%       
%       \quad|\conservedresidues{White}{Blue}{upper}{bf}|: the conserved
%       residues are printed as bold face white uppercase letters on blue.
%       \bigskip
%       
%       \quad|\nomatchresidues{}{}{{$\bullet$}}{}|: instead of the non 
%       matching residues a `$\bullet$' is printed. The colors and style 
%       are not changed.
%       Note the double curly braces which make \TeXshade{} 
%       interpret this complex symbol description as one single 
%       character.
%       \bigskip
%       
%       
%    \item |\shadingmode[|\meta{allmatchspecial/number}|]{similar}|
%    
%       \label{Lsimilarresidues}
%       See \ref{similar} for an example output and an explanation
%       of the shading. In addition to the described commands
%       for changing shading colors this shading mode provides 
%       the command |\similarresidues|.
%       Use it in analogy to the commands above.
%       
%       \label{Lpepsims}\label{Lpepgroups}
%       \label{LDNAsims}\label{LDNAgroups}
%       How does \TeXshade{} know which residues are
%       considered to be similar? These definitions are set by two command
%       couples, i.\,e.\ 
%       |\pepsims|,|\pepgroups| for peptides and
%       |\DNAsims|,|\DNAgroups| for nucleotides. With |\pepsims| and
%       |\DNAsims| residues are defined which are similar to the 
%       consensus residue. Examples:
%       
%       \quad |\pepsims{S}{TA}|\quad If a serine is the consensus
%             residue then all threonins and alanines at this
%             position are shaded in the color for similars. This
%             definition does \emph{not} imply that threonine and
%             alanine are similar to each other! This becomes 
%             obvious when you inspect the next definition:
%             
%       \quad |\pepsims{T}{S}|\quad  Serine but not alanine is declared
%             to be similar to threonine.
%             
%       What happens if there is no consensus residue? How does
%       \TeXshade{} decide if a group of similars is greater than
%       the threshold? For this groups are pre-defined:
%       
%       \quad |\pepgroups{FYW,ILVM,RK,DE,GA,ST,NQ}| This command allows
%             one to set up to nine groups of similars, separated by commas. 
%             Each residue can belong to only one group. If one residue
%             is assigned to several groups only the last assignment is 
%             carried out.
%             
%       \quad |\DNAgroups{GAR,CTY}| This command is used in analogy to
%             the amino acid groups. Here, two ambiguity codes (`R' for
%             pu\underline{r}ine base and `Y' for p\underline{y}rimidine
%             base) are assigned in addition.
%             
%       Residues which do not appear in any of the four commands are 
%       considered not to belong to a group. The default 
%       settings for similars are listed below:
%       \bigskip
%       
%       \begin{verbatim}
% \pepgroups{FYW,ILVM,RK,DE,GA,ST,NQ}
%       
% \pepsims{F}{YW}  % Y and W are similar to F
% \pepsims{Y}{WF}  % W and F are similar to Y
% \pepsims{W}{YF}  % Y and F are similar to W
%    
% \pepsims{I}{LVM} % L, V and M are similar to I
% \pepsims{L}{VMI} % V, M and I are similar to L
% \pepsims{V}{MIL} % M, I and L are similar to V
%    
% \pepsims{R}{KH}  % K and H are similar to R
% \pepsims{K}{HR}  % H and R are similar to K
% \pepsims{H}{RK}  % R and K are similar to H
%       
% \pepsims{A}{GS}  % G and S are similar to A
% \pepsims{G}{A}   % A (but not S) is similar to G
%       
% \pepsims{S}{TA}  % T and A are similar to S
% \pepsims{T}{S}   % S (but not A) is similar to T
%    
% \pepsims{D}{EN}  % E and N (but not Q) are similar to D
% \pepsims{E}{DQ}  % D and Q (but not N) are similar to E
% \pepsims{N}{QD}  % Q and D (but not E) are similar to N
% \pepsims{Q}{NE}  % N and E (but not D) are similar to Q
%    
% \DNAgroups{GAR,CTY}
%       
% \DNAsims{A}{GR}  % G and R are similar to A
% \DNAsims{G}{AR}  % A and R are similar to G
% \DNAsims{R}{AG}  % A and G are similar to R
%       
% \DNAsims{C}{TY}  % T and Y are similar to C
% \DNAsims{T}{CY}  % C and Y are similar to T
% \DNAsims{Y}{CT}  % C and T are similar to Y
%       \end{verbatim}
%
%       
%    \item |\shadingmode[|\meta{filename}|]{T-Coffee}|
%       
%       Enter a \meta{filename} to load the shading
%       information from a |T-Coffee| |score_ascii| file (|www.tcoffee.org|); 
%       see example in \ref{TCoffee}. Make sure
%       that the alignment file specified in the |\texshade| command
%       and this shading file correspond to each other.
%    
%       If you do not enter a \meta{filename} here, a separate
%       command |\includeTCoffee{|\meta{filename}|}| must be used.
%    
%       |T-Coffee| shading can also be used in the consensus
%       p.\,\pageref{Lshowconsensus} and in the feature lines,  
%       in particular color scales and bar plots p.\,\pageref{Lgraphs}, 
%       for the display of shading information.
%    
%       
%    \item |\shadingmode[|\meta{seqref}|]{diverse}|
%    
%       \ref{diverse} depicts an example alignment. Choose the 
%       number or the name of the sequence \meta{seqref} which will be treated
%       as the consensus and to which the other sequences are compared. 
%       If no \meta{seqref} is declared the first sequence is set as 
%       consensus (\meta{seqref} = 1).
%       
%       Standard definitions for |diverse| 
%       mode are:
%
%       \begin{verbatim}
%          \nomatchresidues{Black}{White}{lower}{up}
%          \similarresidues{Black}{White}{lower}{up}
%          \conservedresidues{Black}{White}{{.}}{up}
%          \allmatchresidues{Black}{White}{{.}}{up}
%          \gapchar{-}
%       \end{verbatim}
%   
%       After calling |\shadingmode{diverse}| these commands can be 
%       used to redefine the |diverse| mode settings (mind the double 
%       curly braces around the dot-symbol!). 
%    
%    \item |\shadingmode[|\meta{type}|]{functional}|\label{funcdef}
%       There are seven different functional shading modes available for
%       peptide sequences; nucleotide sequences can not be shaded due
%       to functional aspects. Five of \TeXshade's functional modes
%       correspond to the four `alphabets' employed by \textsc{Karlin} 
%       and \textsc{Ghandour} for peptide alignments [2] or by the
%       rasmol software. Additional 
%       `alphabets' to the standard 20-letter array of amino acids
%       can highlight peptide similarities which were otherwise not visible.
%       For the `alphabet' definitions see below:
%       
%       \begin{itemize}
%       \item \meta{type} = |charge|\quad Acidic (D, E) and basic (H, 
%                           K, R).
%    
%       \item \meta{type} = |hydropathy|\quad Acidic and basic (as 
%                           above), polar uncharged (C, G, N, Q, S, 
%                           T, Y) and hydrophobic nonpolar (A, F, I, L, M, 
%                           P, V, W), see also \textsc{Kyte} and 
%                           \textsc{Doolittle} [3].
%    
%       \item \meta{type} = |structure|\quad External (D, E, H, K, N, Q, R),
%                           internal (F, I, L, M, V) and ambivalent (A, C,
%                           G, P, S, T, W, Y).
%       
%       \item \meta{type} = |chemical|\quad Acidic (D, E), aliphatic
%                           (I, L, V), aliphatic (small) (A, G), 
%                           amide (N, Q), aromatic
%                           (F, W, Y), basic (H, K, R), hydroxyl
%                           (S, T), imino (P) and sulfur (C, M).
%                           
%       \item \meta{type} = |rasmol|\quad (D, E), (K, R, H), (F, Y, W),
%                           (A, G), (C, M), (S, T), (N, Q), (I, L, V), 
%                           (P).
%                           
%       \end{itemize}
%                           
%       The two modes described below highlight sidechain sizes and 
%       hydrophobicity, respectively, according to \textsc{Rose} 
%       \emph{et al.}\ [4,5]. Standard area stands for the surface area
%       of the residue in \AA$^2$, i.\,e. it is a measure for the size
%       of a residue's sidechain. The accessible area value (also in 
%       \AA$^2$) gives information about the size of the surface area
%       which is accessible by solvent molecules within the folded 
%       protein. A very small area means that the residue is
%       strongly buried and is thus very hydrophobic. Hydrophilic
%       residues in turn possess large accessible areas due
%       to their prefered location at the protein surface. Therefore,
%       this kind of shading provides another method, in addition
%       to |hydropathy| and |structure|, for the
%       visualization of structural protein properties.
%       
%       \begin{itemize}
%       
%       \item \meta{type} = |standard area|\quad for the area values
%                           see legend of the alignment in \ref{starea}
%                           
%       \item \meta{type} = |accessible area|\quad for values see
%                           \ref{accarea}
%       
%       \end{itemize}
%       
%       \label{Lclearfuncgroups}
%       If no \meta{type} or an unknown \meta{type} is designated as option
%       all functional groups and shading colors are cleared. This is
%       also achieved by the command 
%       |\clearfuncgroups|. With all groups cleared one can start to
%       build new shading modes from scratch. How to do this is explained
%       in the next section.
%       
%    \label{Lfuncshadingstyle} 
%    In order to exchange the colors but to keep the group definitions
%    and descriptions the command 
%    |\funcshadingstyle| can be
%    employed. Usage:
%    \medskip
%    
%    \quad|\funcshadingstyle{|\meta{residue}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}|
%    
%    \hfill|{|\meta{case}|}{|\meta{style}|}|
%    \medskip
%    
%    \meta{residue} is one representative of the whole amino acid group. The 
%    colors which are declared by the next four parameters are used 
%    for all residues in this group. \meta{case} and \meta{style} are 
%    as described for example in |\nomatchresidues|.
%    \end{enumerate}
%    
%       With |\shadeallresidues| \label{Lshadeallresidues} the 
%       threshold is ignored and
%       all residues are shaded due to their group assignment.
%
%    \subsection{Creating new functional shading modes}
%    
%    The grouping of amino acids due to other properties can make sense as
%    suggested by \textsc{Karlin} and \textsc{Ghandour} [2], e.\,g.\ 
%    physical properties (molecular weight, shape), kinetic properties
%    (reaction velocity, Michaelis-Menton constant), or structure
%    ($\alpha$-helices, $\beta$-sheets, turns).
%    
%    \label{Lfuncgroup}
%    New amino acid groups are defined with the
%    |\funcgroup| command. This command needs six parameters:
%    \medskip
%    
%    \quad|\funcgroup{|\meta{descr}|}{|\meta{residues}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}|
%    
%    \hfill|{|\meta{case}|}{|\meta{style}|}|
%    \medskip
%    
%    \meta{descr} contains descriptive text which is displayed in the legend.
%    The second parameter \meta{residues} holds the amino acids to be
%    grouped. The colors for the foreground and background are set 
%    with the following two parameters, the case and style is declared by the 
%    last parameters. The example below defines a 
%    funcional group named `acidic ($-$)' containing the amino acids
%    aspartic and glutamic acid with white letters on a red background:
%    \bigskip
%    
%    \quad|\funcgroup{acidic ($-$)}{DE}{White}{Red}{upper}{up}|
%    \bigskip
%    
%    For the usage of colors see section \ref{colors}. Up to nine
%    individual groups can be defined. New groups are simply added to the
%    already existing groups, i.\,e.\ if an extension of the group
%    definitions of an existing shading mode is desired there is
%    no need to clear these groups und re-define them again. Just 
%    add the new groups with the |\funcgroup| command. To create 
%    completely new modes use the command
%    |\shadingmode{functional}| without an option 
%    \emph{before} setting the new groups. The new definitions are active
%    only in the functional shading mode---so be sure to
%    have it switched on before setting the new groups.
%    Remember, |\shadingmode{functional}| without an optional parameter
%    clears all groups defined before, see above. The following example
%    shows the definitions needed to produce an output which is identical 
%    to the functional mode `charge':
%    \bigskip
%    
%    \quad|\begin{texshade}{|\meta{alignmentfile}|}|
%    \medskip
%    
%    \quad\quad |\shadingmode{functional}|
%    
%    \quad\quad |\funcgroup{acidic ($-$)}{DE}{White}{Red}{upper}{up}|
%    
%    \quad\quad |\funcgroup{basic ($+$)}{HKR}{White}{Blue}{upper}{up}|
%    \medskip
%    
%    \quad|\end{texshade}|
%    
%    
%    \subsection{Appearance of the consensus line}
%    
%    \label{Lthreshold}
%    An important parameter for the calculation of the consensus is the
%    threshold percentage. Default setting is 50\%, i.\,e.\ to become
%    the consensus residue more than half of the residues at this
%    position must be identical or similar, depending on the shading
%    mode. Any percentage between 0 and 100 is allowed and can be 
%    set with 
%    |\threshold{|\meta{percentage}|}|, e.\,g.\ |\threshold{50}|.
%
%    Additionally, an optional parameter can be set, e.\,g.\,
%    |\threshold[90]{50}|, to label residues that are highly conserved
%    in a special color (see example on page \pageref{ident}).
%    
%    \label{Lconstosingleseq}
%    Another possibility is to set one sequence of the alignment
%    as consensus and 
%    compare the other sequences to this one. Therefore, the
%    command 
%    |\constosingleseq{|\meta{seqref}|}| is provided. The
%    \meta{seqref} selects the sequence to be used as consensus
%    (numbering according to the appearance in the alignment file;
%    top sequence is number~1, or use the sequence name). 
%    Nevertheless, the threshold percentage is also taken into 
%    account, i.\,e.\ with a threshold of 50\% half
%    of the sequences must be identical or similar compared to the 
%    specified consensus sequence in order to be shaded.
%    \label{Lconstoallseqs} With |\constoallseqs| the 
%    consensus is calculated considering all sequences (the case 
%    described in the paragraph above).
%    
%    \label{Lshowconsensus}\label{Lhideconsensus}
%    \label{Lnameconsensus}
%    Consensus lines are displayed either on the top or at the bottom
%    of the alignment by calling 
%    \medskip
%
%    |\showconsensus[|\meta{color/scale}|[,|\meta{color/scale}|]]{|\meta{position}|}| 
%    \medskip
%
%    with 
%    \meta{scale} |Gray|, |BlueRed|, |RedBlue|, |GreenRed|, |RedGreen|,
%    |ColdHot| (recommended), |HotCold|, or |T-Coffee| \ref{TCoffee}, and \meta{position} |top| 
%    or |bottom|. 
%
%    The first color defines the foreground, i.e. the letters, the
%    second color---if specified---defines the background. 
%    If a color scale is named the consensus will be shaded according
%    to the level of sequence conservation. For an example see page
%    \pageref{shadecons}. You can find more information on color scales 
%    on page \pageref{Lgraphs}. These scales can be exported as a Pymol
%    [8] \label{Lexportconsensus}
%    script by |\exportconsensus[|\meta{filename}|]{|\meta{seqref}|}|.
%    If no \meta{filename} is specified |export.txt| will be used. The 
%    generated file can be opened in Pymol in order to shade a 3D model
%    of the sequence \meta{seqref}.
%
%    To hide the consensus use 
%    |\hideconsensus|. The consensus
%    line is named `consensus' in english texts, `consenso' in spanish
%    or `Konsensus' if the |german.sty| is used. With 
%    |\nameconsensus{|\meta{name}|}| any name can be set.
%    
%    \label{Ldefconsensus} 
%    You can tell \TeXshade{} which symbols or letters to use in
%    the consensus line for different matching qualities by 
%    \bigskip
%    
%    \quad|\defconsensus{|\meta{symbol1}|}{|\meta{symbol2}|}{|\meta{symbol3}|}|.
%    \bigskip
%    
%    The following parameters are allowed for symobols 1--3:
%    
%    \begin{enumerate}
%    
%    \item \meta{symbol1} = no match symbol (if below threshold)
%    
%          \begin{itemize}
%             \item any character or letter
%             \item |{}| (empty braces) for blank space
%          \end{itemize}
%          
%    \item \meta{symbol2} = conserved symbol (if threshold is exceeded)
%    
%          \begin{itemize}
%             \item |upper| (prints the consensus residue in uppercase)
%             \item |lower| (prints the consensus residue in lowercase)
%             \item any character or letter
%             \item |{}| (empty braces) for blank space
%          \end{itemize}
%          
%    \item \meta{symbol3} = highly conserved symbol (if
%
%                                 \hfill|\allmatchspecial| is active)
%    
%          \begin{itemize}
%             \item see \meta{symbol2}
%          \end{itemize}
%    
%    \end{enumerate}
%    
%    Example: |\defconsensus{{}}{*}{upper}| does not show non matching
%    residues in the consensus line, marks conserved residues 
%    with `|*|', and displays the uppercase letter of the consensus
%    residue at positions with high conservation.
%    
%    
%    \label{Lconsensuscolors}
%    Finally, the colors of the above defined symbols are adjustable
%    by the command: 
%    
%    \begin{tabbing}
%    \quad|\consensuscolors|\=|{|\meta{res.col.1}|}{|\meta{shad.col.1}|}|\\
%    
%    \>|{|\meta{res.col.2}|}{|\meta{shad.col.2}|}|\\
%    
%    \>|{|\meta{res.col.3}|}{|\meta{shad.col.3}|}|\\
%    \end{tabbing}
%    
%    The color definitions are in the same order as in the
%    |\defconsensus| command:
%    
%    \begin{enumerate}
%    
%    \item \meta{res.col.1} = no match residue color (if below threshold)
%    
%          \meta{shad.col.1} = no match background color 
%          
%    \item \meta{res.col.2} = conserved residue color (if threshold is exceeded)
%    
%          \meta{shad.col.2} = conserved background color 
%          
%    \item \meta{res.col.3} = highly conserved residue color (if 
%
%                                 \hfill|\allmatchspecial| is active)
%    
%          \meta{shad.col.3} = highly conserved background color 
%    
%    \end{enumerate}
%    
%    For colors which are not to be changed empty braces can be used.
%    
%    Example:\medskip
%    
%    \quad|\consensuscolors{}{}{Blue}{White}{Red}{Green}|
%    \medskip
%    
%    Non matching symbol colors are not changed, 
%    conserved residues are displayed blue on white and highly conserved residues
%    appear as red symbols on a green background in the 
%    consensus line.
%    
%    \subsection{Display of logos}
%    
%    \subsubsection{Sequence logos}
%    
%    \label{Lshowsequencelogo}\label{Lhidesequencelogo}
%    In a sequence logo [7], the information content $I(P_i)$ of 
%    each alignment position $i$ is defined as 
%
%    \[ 
%    I(P_i) = \log_2 \vert\Sigma\vert + \sum P_{ij} \cdot \log_2 P_{ij}
%    \]
%
%    \noindent
%    with $\vert\Sigma\vert$ being the cardinality of the used alphabet, 
%    i.\,e. 4 for DNA and 20 for protein sequences, and $P_{ij}$ 
%    being the frequency of residue $j$ at this position. Each position 
%    is displayed as a stack of residue symbols whose heights 
%    represent their proportion of the information content (example on
%    p.\pageref{logo}).
%
%    The display of sequence logos can be either on the top or at the bottom
%    of a nucleotide or protein alignment. Logos will be shown after the
%    command: |\showsequencelogo[|\meta{colorset}|]{|\meta{top/bottom}|}|. If no optional
%    \meta{colorset} is selected the residues will be shaded as follows:\medskip
%
%    \begin{itemize}
%    \item Nucleotide sequences
%
%    \begin{itemize}
%      \item[G]: Black
%      \item[A]: Green
%      \item[T,U]: Red
%      \item[C]: Blue
%    \end{itemize}
%    
%
%    \item Protein sequences (similar to rasmol)
%
%    \begin{itemize}
%      \item[D,E]: Red
%      \item[C,M]: Yellow
%      \item[K,R]: Blue
%      \item[S,T]: Orange
%      \item[F,Y]: MidnightBlue
%      \item[N,Q]: Cyan
%      \item[G]:   LightGray
%      \item[L,V,I]: Green
%      \item[A]: DarkGray
%      \item[W]: CarnationPink
%      \item[H]: CornflowerBlue
%      \item[P]: Apricot
%      \item[B,Z]: LightMagenta
%    \end{itemize}
%    \end{itemize}
%    
%    Optional color sets correspond to the functional shading modes
%    |chemical|, |rasmol|, |hydropathy|, |structure|, |standard area|, 
%    |accessible area| (see p.\pageref{funcdef}). The |\showsequencelogo| 
%    command can be reversed by |\hidesequencelogo|.
%
%    \label{Llogocolor}\label{Lclearlogocolors}
%    Logo colors can be turned to `Black' with the command
%    |\clearlogocolors[|\meta{color}|}| with the optional parameter
%    not set. The optional parameter can be used to set all 
%    residue colors to \meta{color}, e.g.\ |\clearlogocolors[Blue]|.
%    User specific logo color sets are defined by using
%    |\logocolor{|\meta{residues}|}{|\meta{color}|}|, e.g.\ 
%    |\logocolor{DE}{Red} \logocolor{CM}{Yellow}| etc.
%
%    \label{Ldofrequencycorrection}\label{Lundofrequencycorrection}
%    It is common practice for protein sequence logos to correct
%    amino acid frequencies to the background frequency in the
%    alignment, which usually differs from the equal distribution
%    of 5\% for each residue. Frequency correction can be turned on
%    by |\dofrequencycorrection| and off by |\undofrequencycorrection|.
%
%    \label{Llogostretch}The vertical extent of the logo can be changed by 
%    |\logostretch{|\meta{factor}|}|, e.g.\ |\logostretch{1.5}|.
%    The width of the logo characters is dependent on the character
%    width set for the alignment, see |\charstretch| on p.\pageref{Lcharstretch}.
%
%    \label{Lshowlogoscale}\label{Lhidelogoscale}Finally, the bit-scale 
%    can be turned off and on using |\hidelogoscale| and
%    |\showlogoscale[|\meta{color}|]{|\meta{position}|}|, respectively, with
%    \meta{position} |left|, |right|, or |leftright| and an optional
%    \meta{color}. 
%    \label{Lnamesequencelogo}
%    A name for the sequence logo can be set, which is displayed
%    next to the scale by |\namesequencelogo{|\meta{name}|}|.
%
%
%    \subsubsection{Subfamily logos}
%
%    Subfamily logos provide a novel tool to visualize
%    subfamily-specific sequence deviations at alignment positions with
%    a high information content in an intuitive way [14].
%
%    This is achieved by subtracting from the frequency of a residue within 
%    a pre-defined subset of sequences, i.\,e. a subfamily, the frequency of 
%    this residue in the remaining set of sequences. The difference is then 
%    weighted by the information content, see above section on sequence logos.
%    An example is shown on p.\pageref{sublogo}.
%
%    Subtraction of frequencies produces values from $-1$ to $1$. Positive 
%    values correspond to residues which are characteristic for the subfamily 
%    (shown upright in the output), negative values to those that are typical 
%    for the remaining sequences (shown upside-down). Positions with an equal 
%    distribution of the residue result in a zero value. 
%
%    \label{Lshowsubfamilylogo}\label{Lhidesubfamilylogo}\label{Lsetsubfamily}
%    Subfamily logos are displayed analogous to sequence logos by the command 
%    |\showsubfamilylogo[|\meta{colorset}|]{|\meta{top/bottom}|}| and hidden by
%    |\hidesubfamilylogo|. To calculate a subfamily logo, it is further required
%    to define a subfamily within the alignment by 
%    |\setsubfamily{|\meta{seqrefs}|}|, e.g. |\setsubfamily{1-10,20,AQP3}|. 
%
%    For coloring residues, display/stretching of the scales, and frequency 
%    correction the same commands as for sequence logos apply with two exceptions.
%    \label{Lshownegatives}\label{Lhidenegatives}
%    First, subfamily logos contain negative values, which can be displayed
%    |\shownegatives[|\meta{weak, medium, strong}|]| or hidden 
%    |\hidenegatives|. Without the optional parameter negative residues will
%    be tinted by 50\%, i.e. |medium|. This greatly improves readability. 
%    \label{Lnamesubfamilylogo}
%    Second, a name for the subfamily logo is set by 
%    |\namesubfamilylogo[|\meta{neg.name}|]{|\meta{pos.name}|}| with a required
%    name for the positive part of the logo and an optional name for the negative
%    part.
%
%    \label{Lrelevance}\label{Lshowrelevance}\label{Lhiderelevance}
%    In order to better recognize relevant positions in the subfamily logo, a 
%    bit-value can be set above which the deviation is considered relevant
%    by the command |\relevance{|\meta{bit-value}|}|. If this command is
%    not given 2.321\,bit is assumed for proteins, i.\,e.
%    $\log_2 5$, and 1\,bit for DNA, i.\,e. $\log_2 2$. Such positions will 
%    be labeled by 
%    |\showrelevance[|\meta{color}|]{|\meta{symbol}|}|, e.\,g.
%    |\showrelevance[Blue]{$\nabla$}|. The symbol will be hidden with
%    |\hiderelevance|. 
%
%    \subsection{Appearance of the sequence lines}
%    
%    \label{seqlines}
%    
%    \subsubsection{Names, numbers and gaps}
%     \label{Lshownames}\label{Lshownumbering}
%    Many parameters that influence the appearance of the actual sequence
%    lines can be changed for customization.
%    Thus, the sequence names can be shown colored via \meta{color}
%    either left or right by
%    \medskip
%    
%    \quad|\shownames[|\meta{color}|]{|\meta{position}|}|
%    \medskip
%
%    with \meta{position} set to |left| or |right|. The numbering can be
%    displayed either left or right and even on both sides by
%    \medskip
%    
%    \quad|\shownumbering[|\meta{color}|]{|\meta{position}|}|
%    \medskip
%    
%    with \meta{position} |left|, |right| or |leftright|. Both,  
%    names and numbering can be displayed on the same side.     
%    \label{Lnamescolor}\label{Lnumberingcolor}    
%    The colors can also be set with |\namescolor{|\meta{color}|}| and 
%    |\numberingcolor{|\meta{color}|}|, respectively. 
%
%    \label{Lnameseq}
%    \TeXshade{} uses the sequence names from the 
%    alignment input file. This can cause some
%    problems during the \TeX-run when special characters are present
%    in those names! \TeXshade{} does not accept the following characters
%    in sequence names: |\ { } @| spaces and the tilde. Those have to be replaced in 
%    the input file. The characters |#| and |%| can only be used with a
%    leading backslash, e.\,g. |\#|. This must also be changed in the
%    input file. All other special characters should be displayed 
%    properly.    
%    
%    Sequence names that are accepted by \TeXshade{} can further be
%    changed in the |texshade| environment: 
%    \medskip
%    
%    \quad|\nameseq{|\meta{seqref}|}{|\meta{name}|}| 
%    \medskip
%    
%    \meta{seqref} selects the sequence whose name is to be changed. 
%    The basis for the \meta{seqref} is the appearance in
%    the alignment input file with the top sequence = 1, or the old 
%    name. 
%    \label{Lnamecolor}\label{Lnumbercolor}    
%    In order to change the colors only of some sequence names or numbers 
%    the commands 
%    |\namecolor{|\meta{seq1}|, ... ,|\meta{seq n}|}{|\meta{color}|}| and 
%    |\numbercolor{|\meta{seq1}|, ... ,|\meta{seq n}|}{|\meta{color}|}| 
%    are provided.
%    
%    \label{Lhidenames}\label{Lhidename}
%    \label{Lhidenumbering}\label{Lhidenumber}
%     In order to hide all names or the numbering use the command
%     |\hidenames| or |\hidenumbering|. If only the names or numbers of
%     some sequences should be hidden apply 
%     
%     |\hidename{|\meta{seq1}|, ... ,|\meta{seq n}|}| or
%     
%     |\hidenumber{|\meta{seq1}|, ... ,|\meta{seq n}|}|, respectively.
%    
%    \label{Lstartnumber} \label{Lallowzero} \label{Ldisallowzero}
%    In some situations, e.\,g.\ when only sections of sequences are 
%    displayed, one
%    may not want to have the residue numbering start out with number~1.
%    The command 
%    |\startnumber[|\meta{start..stop}|]{|\meta{seqref}|}{|\meta{startnumber}|}|
%    allows one to set the starting number of any sequence to any value
%    incl.\ negative values but except `0' which is not usually used in
%    sequence numbering (the transition from negative to positive
%    values is like this: \ldots\ $-2$, $-1$, 1, 2 \ldots). If, however,
%    the use of the number `0' is wanted as sometimes in sequence logos
%    this can be turned on by |\allowzero| and off with |\disallowzero|.
%    The optional parameter can be used to truncate the sequence display
%    to a certain section (see also |\setends| below). 
%    
%    \label{Lseqlength}
%    \TeXshade{} needs to know the correct length of the sequences
%    to be able to break them right after the last residue. If
%    MSF files are used as an input the length is already given
%    but the calculation is usually wrong because the gaps are
%    also counted. Thus, \TeXshade{} counts the number of residues
%    during each run by itself and stores the values in the |.aux| file. That
%    means that it needs two runs to get the numbers right. Again,
%    this is only important if the gap symbol after the sequence end
%    should be suppressed, see below (|\hideleadinggaps|).
%    
%    If you know the correct length of the sequences you can use the
%    command 
%    \medskip
%    
%    \quad|\seqlength{|\meta{seqref}|}{|\meta{length}|}| 
%    \medskip
%    
%    in order to set the values by hand and have the gaps break 
%    properly already in the first \TeX{} run.
%    \medskip
%    
%    Example: |\seqlength{1}{346}| means that sequence no.~1 is 346 
%    residues long.
%    
%    
%    \label{Lsetends}
%    \TeXshade{} can display a section of the complete alignment
%    without the need to edit the alignment input file or even 
%    to re-calculate
%    the entire alignment. This allows one to use one single 
%    alignment of the full length proteins or open reading frames for
%    multiple visualizations of different sections in a document as
%    done in this manual. Thus, the file |AQPpro.MSF| contains
%    the full-length multiple protein alignment of five aquaporins but
%    only sections are displayed as examples in 
%    \ref{ident} through \ref{accarea}. The definition of a section
%    is done by  
%    \medskip
%    
%    \quad|\setends[|\meta{startnumber}|]{|\meta{seqref}|}{|\meta{start..stop}|}|.
%    \medskip
%    
%    Again, \meta{seqref} is the sequence number based on the 
%    appearance in the alignment file, or the name; further, in order to use
%    the consensus as a measure for the sequence section the
%    string `|consensus|' as \meta{seqref} is accepted. The 
%    specified sequence is truncated at
%    positions \meta{start} and \meta{stop}. All other 
%    sequences are cut accordingly. If the number of the first
%    residue in the sequence is set to a new value with the 
%    |\startnumber| command (s.\,a.) this is taken into account. The 
%    \meta{startnumber} can be set as an optional parameter directly
%    in the |\setends| command as well.
%    \medskip
%
%    Some examples:
%    \medskip
%    
%    \quad a) |\setends{1}{21..100}|
%    \medskip
%    
%    \quad b) |\startnumber{1}{101} \setends{1}{121..200}|
%    \medskip
%    
%    Both commands select the same sequence section from the alignment but
%    numbering for sequence 1 starts at position~21 in the first example and at 
%    position~121 in the latter.
%    \medskip
%    
%    \quad c) |\setends[101]{1}{121..200}| equals example b.
%    \medskip
%    
%    \medskip
%    
%    \quad d) |\startnumber[121..200]{1}{101}| also equals example b.
%    \medskip
%    
%    \medskip
%    
%    \quad e) |\setends{consensus}{21..100}|
%    \medskip
%    
%    This may describe a very different section of the multiple
%    sequence alignment because the consensus counts every position
%    including gaps.
%    
%     \label{Lshowruler}\label{Lhideruler}
%     \label{Lrulersteps}\label{Lrulercolor}
%     \label{Lrotateruler}\label{Lunrotateruler}
%     \label{Lnamerulerpos}
%     Another possibility to label sequence positions is to switch
%    on a ruler on the top or at the bottom of the sequence block
%    using \label{ruler}
%    |\showruler[|\meta{color}|]{|\meta{position}|}{|\meta{seqref}|}|. 
%    The residue ruler of one sequence \meta{seqref} or the consensus 
%    (declare `|consensus|' as \meta{seqref}) can be 
%    displayed at \meta{position} |top| or |bottom|.
%    The ruler is hidden with  |\hideruler|. The steps between two
%    numbers are set by |\rulersteps{|\meta{number}|}|. If the steps
%    are set to be very close ($< 4$) or when every position is numbered, the
%    numbering is automatically rotated by 90$^\circ$. Using |\rotateruler|
%    and |\unrotateruler| this can be done and undone manually. 
%    In order to change the
%    ruler color use the optional parameter or the command 
%    |\rulercolor{|\meta{color}|}|. Also, the label and its color at individual 
%    ruler positions can be changed by the user to a string using 
%    |\namerulerpos{|\meta{number}|}{|\meta{text}|[|\meta{color}|]}| 
%    (see example on p.\ \pageref{ras}).
%    
%    \label{Lgapchar}\label{Lgaprule}
%    \label{Lgapcolors}\label{gapchar}
%    Further, the symbol which is displayed in sequence gaps is freely 
%    selectable with  
%    |\gapchar{|\meta{symbol}|}|. \meta{symbol} can be any character
%    or symbol. If math symbols are to be used math mode must be
%    activated by |$| characters, i.\,e. |\gapchar{{$\triangle$}}|.
%    Note the double curly braces in the last command. Everytime a
%    `complex' character is used, i.\,e. a character definition consisting 
%    of more than one letter, it must be braced in order to be interpreted as one 
%    character. One exception is |\gapchar{rule}|; with this 
%    parameter lines are drawn in the sequence gaps with a certain 
%    thickness defined by |\gaprule{|\meta{thickness}|}|, e.\,g.
%    |\gaprule{1.5pt}|. The colors of the gaps and gap symbols are set by 
%    |\gapcolors{|\meta{symbol color}|}{|\meta{background color}|}|.
%    
%    There are some discussions whether or not to display gap symbols before
%    and after the actual sequence. Since v1.3a one can control the
%    appearance of those gap symbols by the commands
%    \label{Lshowleadinggaps} \label{Lhideleadinggaps}
%    |\showleadinggaps| and |\hideleadinggaps|. By default, leading 
%    gaps are indicated by symbols despite my personal
%    thinking that it could suggest that 
%    there are some not displayed residues upstream resp.\ downstream of the 
%    gap.
%    
%    
%    
%    \subsubsection{Hiding, killing, separating and ordering}
%    
%    \label{kill}
%    
%    \label{Lhideseq}\label{Lhideseqs}\label{Lshowseqs}\label{Lkillseq}
%    If one or more sequences from the alignment input file should be used for
%    the calculation of the consensus but it is desired not to
%    display these sequences in the final output use the command 
%    |\hideseq{|\meta{seq1}|,|\meta{seq2}|,|\ldots|,|\meta{seq n}|}|. 
%    For consecutive sequence numbers a dash can be used, e.\,g. 
%    |\hideseq{1-3}| instead of |\hideseq{1,2,3}|. Decending series 
%    are also permitted, e.\,g. |\hideseq{3-1}|.
%    This command allows one for example to hide 
%    the sequence which has been defined as the consensus sequence
%    with |\constosingleseq|. When all sequences should be hidden, e.g. to
%    show a sequence logo alone, one can simply say |\hideseqs|. This
%    command is reversed by |\showseqs|.
%
%    In order to completely exclude sequences the command 
%    |\killseq{|\meta{seq1}|,|\meta{seq2}|,|\ldots|,|\meta{seq n}|}| is 
%    provided. Again, for number series the dash can be used (s.\,a.). The 
%    designated sequences are neither displayed nor
%    considered for the calculation of the consensus. This is
%    another possibility to comment out sequences in addition
%    to the use of an exclamation point infront of the |Name:|
%    definition in an MSF-file (see figure on page \pageref{commout}).
%    
%    \label{Ldonotshade}
%    The command 
%    |\donotshade{|\meta{seq1}|,|\meta{seq2}\ldots|,|\meta{seq n}|}| 
%    makes 
%    one or more sequences (remember the dash, s.\,a.) appear unshaded 
%    in black letters on white background.
%    This does not influence any other sequences or the consensus
%    calculation.
%    
%    \label{Lhideresidues}\label{Lshowresidues}
%    If a very graphical output of the sequences is desired, the 
%    residue symbols or letters can be blanked out by
%    |\hideresidues|. Now, only the shaded boxes are printed. 
%    In combination with |\gapchar{rule}| one obtains alignments
%    in a style \`a la Mondrian.
%    The residues reappear with |\showresidues|.
%    
%    \label{Lseparationline}\label{Lsmallsep}
%    \label{Lmedsep}\label{Lbigsep}
%    \label{Lvsepspace}
%    If an alignment contains members of several subgroups of a
%    protein or a gene family it may be rather helpful to visualize the group
%    divisions by a separation line. Therefore, the command
%    |\separationline{|\meta{seqref}|}| is applicable. This 
%    command inserts vertical space after the sequence which is
%    refered to by \meta{seqref}. How much space is inserted
%    is defined by one of the following commands: 
%    |\smallsep|, |\medsep| (default) or |\bigsep|. These lengths
%    correspond to the known |\small|-, |\med|- and |\bigskip| commands. 
%    With |\vsepspace{|\meta{length}|}| any length with any
%    \TeX{} unit can be assigned, e.\,g. |\vsepspace{2mm}|.
%    
%    \label{Lorderseqs}
%    The sequence order given by the alignment input file is easily
%    reorganized by 
%    |\orderseqs{|\meta{seq1}|,|\meta{seq2}|,|\ldots|,|\meta{seq n}|}|
%    without the need for editing the alignment input file (which 
%    would be a big copy'n'paste job).
%    Make sure that all sequences are assigned in this
%    command. If there are more sequences present than numbers or names in the
%    command an error message will occur. Here also, the dash can be 
%    used for sequence number series. Example: |\orderseqs{1-3,6-4,7}| 
%    is equivalent to |\orderseqs{1,2,3,6,5,4,7}|.
%    Reordering of sequences only changes the output; all commands using
%    the parameter \meta{seqref} are not influenced, because \meta{seqref} 
%    always corresponds to the appearance in the alignment file. Thus, 
%    to completely reverse the order of a five sequence alignment simply type 
%    |\orderseqs{5-1}|.
%    
%    
%    \subsubsection{Residues per line and further settings}
%    
%    \label{Lresiduesperline}\label{Lresiduesperline*}
%    By default \TeXshade{} puts the highest possible by five 
%    divisible number of residues in one line depending on the 
%    |\textwidth|. With |\residuesperline{|\meta{number}|}| a new 
%    value can be set. If this value exceeds the highest possible 
%    number of residues per line it is ignored; lower values are
%    accepted of course. But also in the latter case the number
%    of residues printed per line is rounded such to be divisible by five. 
%    To force \TeXshade{}
%    to set lines with exactly the desired number of residues use
%    the asterisk-extended command |\residuesperline*{|\meta{number}|}|. 
%    Expect multiple
%    \emph{overfull hbox} errors after this command, because in this
%    mode \TeXshade{} does not check the length of the lines any
%    more.
%    
%    \label{Lcharstretch}\label{Llinestretch}
%    \TeXshade{} calculates the dimensions of a shaded box from
%    the width and height of the uppercase letter `M' and the depth of
%    the lowercase `g'. Depending on the font used for the
%    sequence residues the box dimensions might not be fully
%    satisfactory. With |\charstretch{|\meta{factor}|}| and
%    |\linestretch{|\meta{factor}|}| the width and height/depth,
%    respectively, of the boxes can be multiplied individually by a 
%    \meta{factor} to stretch ($>1$) or shrink ($<1$) the dimensions.
%    
%    \label{Lnumberingwidth}
%    The reserved space for the sequence numbering is set by the
%    command |\numberingwidth{|\meta{n digits}|}|. Here, the default setting
%    is four-digit numbering, i.\,e.\ $-999$ through 9999. If this range
%    is to be changed assign the desired number as parameter
%    \meta{n digits}, e.\,g.\ |\numberingwidth{111111}| reserves
%    space for 6 digit numbering.
%    
%    The vertical space between the sequence blocks can be controlled
%    by the commands |\smallblockskip|, |\medblockskip| (default 
%    setting), 
%    \label{Lsmallblockskip}\label{Lmedblockskip}