\documentclass{article}

\usepackage{german}
\usepackage[latin1]{inputenc}

\usepackage{texshade}

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%%% standard: similarity
%\newcommand{\shmode}{}

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%\newcommand{\shmode}{\shadingmode{functional}}

%%% functional, hydrophathy (using amino acid groups)
\newcommand{\shmode}{\shadingmode[hydropathy]{functional}}

\begin{document}

\section{Scores}

\subsection{BAliBASE}
\begin{verbatim}
SP-Score for 5 sequences: 1657
Statistics:
gap-gap:     ( score 0 ) 188
gaps:        ( score 2 ) 216
mismatches:  ( score 1 ) 1225
matches:     ( score 0 ) 991
\end{verbatim}

\subsection{Modified}
\begin{verbatim}
SP-Score for 5 sequences: 2482
Statistics:
gap-gap:     ( score 0 ) 107
gaps:        ( score 2 ) 198
mismatches:  ( score 1 ) 2086
matches:     ( score 0 ) 139
\end{verbatim}

\subsection{MSA-optimal}
\begin{verbatim}
SP-Score for 5 sequences: 1436
Statistics:
gap-gap:     ( score 0 ) 0
gaps:        ( score 2 ) 0
mismatches:  ( score 1 ) 1436
matches:     ( score 0 ) 1164
\end{verbatim}

\subsection{DIALIGN 2.2}
\begin{verbatim}
SP-Score for 5 sequences: 1479
Statistics:
gap-gap:     ( score 0 ) 0
gaps:        ( score 2 ) 0
mismatches:  ( score 1 ) 1479
matches:     ( score 0 ) 1251
\end{verbatim}

\subsection{CLUSTAL W}
\begin{verbatim}
SP-Score for 5 sequences: 1646
Statistics:
gap-gap:     ( score 0 ) 190
gaps:        ( score 2 ) 212
mismatches:  ( score 1 ) 1222
matches:     ( score 0 ) 996
\end{verbatim}

\newpage

\section{Alignments}
\subsection{BAliBASE}

\begin{texshade}{5ptp.msf}
\shmode
\hideconsensus
\end{texshade}

\newpage

\subsection{Modified}

\begin{texshade}{5ptp.modified.msf}
\shmode
\hideconsensus
\end{texshade}

\newpage

\subsection{MSA-optimal}

\begin{texshade}{5ptp.msa.opt.msf}
\shmode
\hideconsensus
\end{texshade}

\newpage

\subsection{DIALIGN 2.2}

\begin{texshade}{5ptp.dialign.msf}
\shmode
\hideconsensus
\end{texshade}

\newpage

\subsection{CLUSTAL W}

\begin{texshade}{5ptp.clustalw.msf}
\shmode
\hideconsensus
\end{texshade}


\end{document}

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