I just found `alv` (https://github.com/arvestad/alv), a tool for viewing multiple sequence alignments on the command line, and it's perfect. I needed a tool to highlight differences and `alv -f fasta -t aa --only-variable aln.afa` does just that. Would prefer the numbering to start at 1 since sequence variants are 1-based #bioinformatics (Data from ERR031940.)