Nigel's Port of the TexShade Package.

Texshade is the display backend for the bioconductor MSA package (and on github):

Texshape has great coloring for amino acids, but is more limited in displaying DNA alignments. I added one of the color brewer color packages to enable better DNA display.

I am tricking the program to generate shading by nucleotide by making this a type of functional annotation. You need to copy the file to a global install as well e.g. sudo cp texshade.sty /usr/local/texlive/2014/texmf-dist/tex/latex/texshade/

Example code to generate MSA plot from R below

source("http://www.bioconductor.org/biocLite.R")
biocLite("msa")
library(msa)
# if a new computer, just edit this file:
system.file("tex", "texshade.sty", package="msa")
dm = readDNAMultipleAlignment("/Users/nigel/pacbio/9320All.fna")
msaPrettyPrint(dm,  shadingMode="functional", showNumbering="none", showLegend=FALSE, askForOverwrite=FALSE, shadingModeArg = "accessible area", shadingColors="blues", consensusColors="BlueRed", showLogo="none", file="All.pdf",y=c(500, 737))
msaPrettyPrint(dm,  shadingMode="functional", showNumbering="none", showLegend=FALSE, askForOverwrite=FALSE, shadingModeArg = "accessible area", shadingColors="blues", consensusColors="BlueRed", showLogo="none", file="GoodSnp.pdf",y=c(586, 592), psFonts=TRUE)
msaPrettyPrint(dm,  shadingMode="functional", showNumbering="none", showLegend=FALSE, askForOverwrite=FALSE, shadingModeArg = "accessible area", shadingColors="blues", consensusColors="BlueRed", showLogo="none", file="BadIndel.pdf",y=c(705, 712), psFonts=TRUE)

And as a pure latex document:

  \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}{/Users/nigel/pacbio/Seq.fasta}
  \seqtype{P}
  \setends{consensus}{500..737}
  \shadingmode[DNA]{functional}
  \showconsensus[BlueRed]{bottom}
  \hidelogoscale
  \shownames{left}
  \nameseq{1}{1}
  \nameseq{2}{2}
  \nameseq{3}{3}
  \nameseq{4}{4}
  \nameseq{5}{5}
  \nameseq{6}{6}
  \nameseq{7}{7}
  \nameseq{8}{8}
  \nameseq{9}{9}
  \nameseq{10}{10}
  \hidenumbering
  \end{texshade}
  \end{document}