We estimate confidence intervals for rates, dates, and tip dates using parametric and non-parametric bootstrap approaches.
By using sampling dates in conjunction with sequence data, it is possible to estimate the rate of evolution, and hence generate phylogenetic trees calibrated in calendar time.
These ‘time-trees’ are more straightforward to interpret in terms of the time to the most recent common ancestor and changes in effective population size, which can then be linked to external epidemiological information, as in the case of the spread of hepatitis C virus in Egypt during antischistosomiasis injection campaigns (Pybus et al.
Such pathogens have been dubbed ‘measurably evolving’ (Drummond et al.
2003), as sequences typically accumulate mutations over epidemiological timescales of years or even months.
A standard approach for assessing uncertainty in phylogenetic analyses is to perform non-PB, in which columns in the multiple sequence alignment are resampled with replacement in order to generate new datasets.