Does the rate estimate include a 95% confidence interval?

Help and Getting Started
1

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.

2

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
image1920×1062 145 KB

e.g. from this build.

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 subcommand:

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