# Fixing the clock rate when refining an H3N2 phylogenetic tree?

**URL:** <https://nextstrain.discourse.group/t/fixing-the-clock-rate-when-refining-an-h3n2-phylogenetic-tree/1462>\
**Category:** Help and Getting Started\
**Created:** [October 28, 2023, 3:24pm UTC](https://nextstrain.discourse.group/t/fixing-the-clock-rate-when-refining-an-h3n2-phylogenetic-tree/1462 "2023-10-28T15:24:38Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Jane](https://avatars.discourse-cdn.com/v4/letter/j/ecb155/32.png) [@Jane](https://nextstrain.discourse.group/u/Jane)\
**Post date:** [October 28, 2023, 3:24pm UTC](https://nextstrain.discourse.group/t/fixing-the-clock-rate-when-refining-an-h3n2-phylogenetic-tree/1462/1 "2023-10-28T15:24:38Z")

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Hi,

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 🙂

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**Author:** ![corneliusroemer](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/corneliusroemer/32/175_2.png) [@corneliusroemer](https://nextstrain.discourse.group/u/corneliusroemer)\
**Post date:** [December 19, 2023, 7:39pm UTC](https://nextstrain.discourse.group/t/fixing-the-clock-rate-when-refining-an-h3n2-phylogenetic-tree/1462/2 "2023-12-19T19:39:50Z")

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Hi Jane! I’m not sure there’s a single correct answer here. I think it depends on what you’re trying to do with the build, over which time scale you have samples.

The Nextstrain-maintained seasonal-flu build fixes the clock rate, see this workflow file: [seasonal-flu/workflow/snakemake\_rules/core.smk at 9a77301b4f9c58a8e948b0f7231134fcc3fe39b8 · nextstrain/seasonal-flu · GitHub](https://github.com/nextstrain/seasonal-flu/blob/9a77301b4f9c58a8e948b0f7231134fcc3fe39b8/workflow/snakemake_rules/core.smk#L215-L264)

The clockrates for all types and segments are defined here: [seasonal-flu/workflow/snakemake\_rules/core.smk at 9a77301b4f9c58a8e948b0f7231134fcc3fe39b8 · nextstrain/seasonal-flu · GitHub](https://github.com/nextstrain/seasonal-flu/blob/9a77301b4f9c58a8e948b0f7231134fcc3fe39b8/workflow/snakemake_rules/core.smk#L183-L213)

I’m not a flu expert so I don’t know about all the caveats here, but this might be a good starting point.

Best,

Cornelius