% preamble
\documentclass[preview]{standalone}
\usepackage{texshade}
\usepackage{inconsolata}
\usepackage[showframe]{geometry}
% begin document
\begin{document}
\begin{texshade}{alignmentFile.txt}
% IDENTITY HIGHLIGHTING
\shadingmode[allmatchspecial]{identical}
\nomatchresidues{Gray70}{White}{upper}{bf}
\conservedresidues{Black}{LightCyan}{upper}{bf}
\allmatchresidues{White}{Red}{upper}{bf}
% CHEMICAL HIGHLIGHTING
%\shadingmode[chemical]{functional}
% STRUCTURAL HIGHLIGHTING
%\shadingmode[structure]{functional}
% HIGHLIGHTING THRESHOLD
\threshold[100]{50} % [high]{low}
% CAPTION - textbf{} specifies bold text
\showcaption[bottom]{\textbf{Protein MSA with Similarity Highlighting}}
% LEGEND
\showlegend
\movelegend{0cm}{0cm} % {Horizontal}{Vertical} offsets
% TOP NUMBERING
%\showruler{1}{top}
%\hidenumbering
% SIDE NUMBERING
\shownumbering
% CONSENSUS
\hideconsensus
% FINGERPRINTING
%\fingerprint{200}
% SEQUENCE LOGO
%\showsequencelogo{top}
%\showlogoscale{leftright}
%\dofrequencycorrection
%\setends{1}{1..200}
% TEXT SIZE (see README)
\namesfootnotesize
\residuesfootnotesize
\legendfootnotesize
\numberingtiny
% end document
\end{texshade}
\end{document}
