Hi, I’m running this command: Shell command: augur refine --tree nextstrain_results/tree_raw.nwk --alignment nextstrain_results/aligned.fasta --metadata phylogeny/genotypes_combined/combined_metadata.tsv --output-tree nextstrain_results/tree.nwk …

In nextstrain_results/branch_lengths.json each node (including internal nodes) will have a numdate (numeric date) value which you can use to plot on a temporal x-axis. Best, james

This works nicely, thanks! So tree.nwk output by augur refine already has time-calibrated branch lengths? And the numdate in the branch_lengts.json is something calculated outside of TimeTree by augur refine?

numdate comes form TreeTime, but augur refine is the wrapper which exports it in the JSON format. The “refined” newick branch lengths are in calendar time, measured in units of clock rate. If you want subs/site divergence you should use the mutation_length property in the JSON (which is what augur e…

How to get the correct time axis when using augur refine and timetree?

jonr February 4, 2026, 10:09am 3

I understand. Thanks, I’ll check it out!

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How to get the correct time axis when using augur refine and timetree?

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