When I generate clocked trees using Augur commands, and view the JSON files in auspice.us, and then click on the ‘DIVERGENCE’ view, the X-axis of the Tree has values like this: 0.00005, 0.00010, 0.00015, etc. But when I go to Nextstrain to view a downsampled global tree of SC2, and set the view to ‘DIVERGENCE’ the X-axis shows me a count of the number of mutations. Is there a simple, straightforward way to get my output to look like that (with the number of mutations)?
Thanks.
Okay, someone else on my team actually RTFM and told me that the augur refine command has an option --divergence-units which you can set to ‘mutations’ so I am test that right now.