We estimate confidence intervals for rates, dates, and tip dates using parametric and non-parametric bootstrap approaches.
This method is implemented as an open-source R package, Pathogen sequence data can provide important information about the timing and spread of infectious diseases, particularly for rapidly evolving pathogens such as RNA viruses.
2, The sampling distribution of estimated rates and time of the most recent common ancestors (TMRCAs) is asymptotically normal and the SD of the sampling distribution is well approximated by the PB distribution of estimated rates and TMRCAs.
The complete algorithm is described in algorithm box 2.
2015) and compare the performance of the new method with other state-of-the-art methods.
Given a lineage with units of substitutions per site, which can be estimated from a sequence alignment using maximum likelihood (ML), a Bayesian approach, or a distance-based approach such as neighbour joining.
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.
Fast approximations to non-PB for phylogenetic reconstruction have also been proposed (Nguyen et al.