Fixing the clock rate when refining an H3N2 phylogenetic tree?


Thanks for creating this platform! I’m just getting started with augur and I have a question about using the “augur refine” command to further improve an H3N2 phylogenetic tree that I built using the “augur tree” command (with FastTree). I noticed that in the Zika tutorial, the clock_rate is fixed to be 0.0008. I wonder in the case of refining an H3N2 tree, is it also a good idea to fix the clock rate (instead of letting treetime estimate the rate from the data)? If so, what would be a suitable number?

Many thanks in advance :slight_smile: