# Does the rate estimate include a 95% confidence interval?

**URL:** <https://nextstrain.discourse.group/t/does-the-rate-estimate-include-a-95-confidence-interval/1455>\
**Category:** Help and Getting Started\
**Created:** [October 26, 2023, 2:57pm UTC](https://nextstrain.discourse.group/t/does-the-rate-estimate-include-a-95-confidence-interval/1455 "2023-10-26T14:57:21Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Jian](https://avatars.discourse-cdn.com/v4/letter/j/7ba0ec/32.png) [@Jian](https://nextstrain.discourse.group/u/Jian)\
**Post date:** [October 26, 2023, 2:57pm UTC](https://nextstrain.discourse.group/t/does-the-rate-estimate-include-a-95-confidence-interval/1455/1 "2023-10-26T14:57:21Z")

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Hi everyone!

I have a question about the “clock” figure. Does the rate estimate displayed provide a 95% confidence interval, similar to using BEAST to analyze the evolutionary rate of a virus, where you obtain both the rate and its 95% confidence interval?

Thank you in advance for your assistance.

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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, 7:44pm UTC](https://nextstrain.discourse.group/t/does-the-rate-estimate-include-a-95-confidence-interval/1455/2 "2023-12-19T19:44:34Z")

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Hi @Jian

I’m not entirely sure about which “clock” figure you’re talking, I’m assuming it’s the “clock” display mode of Auspice, i.e. this view:

 ![image](https://canada1.discourse-cdn.com/flex031/uploads/nextstrain/original/1X/4e3be1819309fe2d74fdac82deee2aa3f1293e82.jpeg)  
e.g. from this [build](https://nextstrain.org/groups/neherlab/ncov/spike-only?c=clade_nextstrain&l=clock).

This tree layout is not meant to provide definitive numbers to be used in reporting, it’s more of a “quick and dirty” estimate.

If you want to get more reliable and statistically valid rate estimates, I recommend to use treetime - if you have created a tree with `augur`, then it’s very easy to plug the metadata and tree files into treetime to get standard errors.

Have a look at the [`treetime clock`](https://treetime.readthedocs.io/en/latest/commands.html#clock) subcommand:

```auto
treetime clock
Calculates the root-to-tip regression and quantifies the ‘clock-i-ness’ of the tree. It will reroot the tree to maximize the clock-like signal and recalculate branch length unless run with –keep-root.

treetime clock [-h] --tree TREE [--rng-seed RNG_SEED] [--dates DATES]
               [--name-column NAME_COLUMN] [--date-column DATE_COLUMN]
               [--sequence-length SEQUENCE_LENGTH] [--aln ALN]
               [--vcf-reference VCF_REFERENCE] [--clock-filter CLOCK_FILTER]
               [--clock-filter-method {residual,local}]
               [--reroot REROOT [REROOT ...] | --keep-root]
               [--tip-slack TIP_SLACK] [--covariation] [--allow-negative-rate]
               [--plot-rtt PLOT_RTT] [--verbose VERBOSE] [--outdir OUTDIR]

```

I hope this helps!

Best,

Cornelius