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nextstrain / augur

Pipeline components for real-time phylodynamic analysis
https://docs.nextstrain.org/projects/augur/
GNU Affero General Public License v3.0
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Branch length units in augur refine output #1522

Open Eric-CH-Chen opened 5 days ago

Eric-CH-Chen commented 5 days ago

Hi All,

I went through the documentation but couldn't find the answer. What is the unit of the branch length of the newick tree from augur refine output? I can't find out what is the appropriate units for describing the units branch length.

In the input, raw_tree from augur tree (iqtree), the branch length is in DNA mutations per site (per manual), but I can't find out if the branch length units is the same in the output. I intuitively thought that it would still be the same but corrected/refined by dates from the meta data, but I just realized that I don't really know for sure. For example, could it be "mutations per site per year"?

Thank you!

jameshadfield commented 5 days ago

The branch lengths in the newick from augur refine are in units of years (assuming you are running with --timetree). The node-data JSON output from augur refine contains more detailed data for each branch including the "mutation_length" (subs/site), date inference of each node etc.