I'm making several figures that contain protein alignments. What are the best tools to use for creating protein alignments that are capable of outputting vector graphics? Ideally, I would like to use MUSCLE for the alignment. I would like to generate alignments and export them as vector graphics. Thanks. In case of sequence alignment, I'd recomment trying out Jalview. There you can save alignments as SVG and EPS files, to and then edit them with either Adobe Illustrator or Inkscape. Good luck. I came across this web-server: http://wavis.img.cas.cz that will take multiple sequence alignments in several different formats (including fasta) and output to several different graphical formats (including SVG). Click on Scheme Drawing on the sidebar to get to the input page. You can use any alignment program you wish, as the actual alignment and visualization are separate tasks. You can use Seaview to run Muscle and edit your MSA as well. The 'prepare PDF' functionality exports the result in a vectorial way. Source.