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.
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.
I would recommend using Jalview (www.jalview.org), it can run the MUSCLE MSA algorithm, then allow you to customize the MSA viewer and export SVG figures. I have added links to YouTube videos about Jalview and how to customise and export figures.