I had a go on Nextalign in my local machine yesterday, great tool. Getting alignments as codon and protein alignments is a plus.
As Nextalign may not yet be available within augur, I was wondering what would be the best way to add it in a environment, so it can be run as a component of a Snakemake workflow.
Following up for future readers to add that nextalign is also included in the nextstrain/base Docker image, for anyone using a containerized workflow (with or without the Nextstrain CLI).