msaPrettyPrintOutput.tex

\documentclass[10pt]{article}

\usepackage{texshade}

\headheight=0pt
\headsep=0pt
\hoffset=0pt
\voffset=0pt
\paperwidth=11in
\paperheight=8.5in
\ifx\pdfoutput\undefined
\relax
\else
\pdfpagewidth=\paperwidth
\pdfpageheight=\paperheight
\fi
\oddsidemargin=-0.9in
\topmargin=-0.7in
\textwidth=10.8in
\textheight=7.9in

\pagestyle{empty}

\begin{document}
\begin{texshade}{/tmp/RtmpJ60r0A/seq620128fe78e5.fasta}
\seqtype{N}
\shadingmode{identical}
\threshold{50}
\showconsensus[ColdHot]{bottom}
\shadingcolors{blues}
\showsequencelogo[chemical]{top}
\hidelogoscale
\shownames{left}
\nameseq{1}{KP29 CL612 TR 1 x 508nt}
\nameseq{2}{KP37 CL673 TR 1 x 508nt}
\nameseq{3}{KP23 CL720 TR 1 x 508nt}
\nameseq{4}{KP34 CL522 TR 1 x 508nt}
\nameseq{5}{KP26 CL662 TR 1 x 508nt}
\nameseq{6}{KP30 CL538 TR 1 x 508nt}
\nameseq{7}{KP33 CL566 TR 1 x 508nt}
\nameseq{8}{KP32 CL792 TR 1 x 508nt}
\nameseq{9}{KP39 CL780 TR 1 x 508nt}
\shownumbering{right}
\showlegend
\end{texshade}
\end{document}