I am trying to figure out if there is any available R method (or other alignment software) to create a clean visualization of a nucleotide alignment such as the one attached. Specifically, I have an alignment of nucleotide sequences in fasta file format and would like to portray the alignment where mismatches and specific mutational signatures are highlighted (i.e. G to A). I am currently using the website http://www.hiv.lanl.gov/cgi-bin/HIGHLIGHT/HIGHLIGHT_XYPLOT/highlight1.cgi to do this but there are limitations and I am hoping for more control over variables such as sizing of the text, mismatch bars, colors, etc.
Any help or comments are always appreciated.