Nextalign + Snakemake

Hi all,

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.

Any suggestions?

Hi Anderson,

you can simply download a binary. See “Downloads” section on

There are branches of ncov that use nextalign. Will hopefully be opt-in on master soon.

This one is built on current (new) master but doesn’t have the protein alignments yet:

This one is diverged and served more as a playground but has the protein alignments:

let us know if you run into issues,


Thank you, @rneher. Good call. I’ll just add the binary inside a scripts folder, and that should work just fine, indeed.

I’ll let you know if I run into any issues.

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).