An example for how to generate a pretty fasta alignment with LaTeX, using the textshade package

README.md

Run using the command pdflatex test.tex

An overleaf document can be found here: https://www.overleaf.com/read/tynwkrwwpfmk When you click on the link you can also the resulting PDF

test.tex

\documentclass[11pt, oneside]{article}   	% use "amsart" instead of "article" for AMSLaTeX format
\usepackage{geometry}                		% See geometry.pdf to learn the layout options. There are lots.
\usepackage{texshade}
\geometry{letterpaper}                   		% ... or a4paper or a5paper or ... 
\usepackage{graphicx}				% Use pdf, png, jpg, or eps with pdflatex; use eps in DVI mode
								% TeX will automatically convert eps --> pdf in pdflatex		
\usepackage{amssymb}

\title{Wonderful title}
\author{Tabea Kischka}

\begin{document}
\maketitle
\section{Pretty Alignment}
\begin{texshade}{test2.fasta}
\showsequencelogo{top}
\end{texshade}


\end{document}  

test2.fasta

>Human
aaaatgcctattggatccaaagagaggccaac-attttttgaaatttttaagacacgctgcaacaa-agc
>Chimp
aaaatgcctattggatccaaagagaggccaac-attttttgaaatttttaagacacgctgcaacaa-agc
>Gorilla
aaaatgcctattggatccaaagagaggccaac-attttttgaaatttttaagacacgctgcaacaa-agc
>Orangutan
aaaatgcctgttggatccaaagagaggccaac-attttttgaaatttttaagacacgctgcaacaa-agc
>Gibbon
aaaatgcctattggatccaaagagaggcaaac-attttttgaaatttttaagacacgctgcaacaa-agc
>Rhesus
aaaatgtctattggatccaaagagaggccaac-attttttgaaatttttaagacacgctgcaacaa-agc
>Crab-eating macaque
aaaatgtctattggatccaaagagaggccaac-attttttgaaatttttaagacacgctgcaacaa-agc
>Baboon
aaaatgtctattggatccaaagagaggccaac-attttttgaaatttttaagacacgctgcaacaa-agc
>Green monkey
aaaatgtctattggatccaaagagaggccaac-attttttgaaatttttaagacacgctgcaacaa-agc
>Marmoset
aaaatgcctattggatccaaagagaggcctac-tttttttgaaatttttaagacacgctgcaacaa-agc
>Squirrel monkey
aaaatgcctattggatccaaagagaggccaac-tttttttgaaatttttaagacacgctgcaacaa-agc
>Bushbaby
aatatgtctgttggatccaaagagaggccaac-tttctttgaaatttttaagacacgatgcaacga-agc
>Chinese tree shrew
aaaatgcccattgaatccaaagagaggccaac-cttttttgaaatttttaagacacaatgcaacca-agc
>Squirrel
aaaatgcctattggatccaaagagaggccaac-tttttttgaaatttttaagacgcgatgcagcgg-agc
>Lesser Egyptian jerboa
aaaatgtctattggatacaag---aggccaac-tttttttgaaatttttaagacgcgatgcagcaa-agc
>Prairie vole
aaaatgcccattgaatacaaaaggagaccaac-tttttttgaaatttttcaggcgcgatgcagcac-agc
>Chinese hamster
aaaatgtccaatgaatacaaaaggagaccaac-tttttttgaaatttttaaggcacgatgcagcac-agc
>Golden hamster
aaaatgcccattgaatacaaa---agaccaac-tttttttgaaatttttaaggcacgatgcagcac-agc
>Mouse
aaaatgcccgttgaatacaaaaggagaccaac-tttttgggaaatttttaaggcgagatgcagcac-agc
>Rat
aacatgaccgttgaatacaaaaggagaccaac-tttttgggaaatttttaaagcgagatgcagcac-agc