Imperial College London

DrErikVolz

Faculty of MedicineSchool of Public Health

Senior Lecturer
 
 
 
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Contact

 

+44 (0)20 7594 1933e.volz Website

 
 
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Location

 

UG10Norfolk PlaceSt Mary's Campus

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Summary

 

Publications

Citation

BibTex format

@article{Volz:2017:ve/vex025,
author = {Volz, EM and Frost, SDW},
doi = {ve/vex025},
journal = {Virus Evolution},
title = {Scalable relaxed clock phylogenetic dating},
url = {http://dx.doi.org/10.1093/ve/vex025},
volume = {3},
year = {2017}
}

RIS format (EndNote, RefMan)

TY  - JOUR
AB - Molecular clock models relate observed genetic diversity to calendar time, enabling estimation of times of common ancestry. Many large datasets of fast-evolving viruses are not well fitted by molecular clock models that assume a constant substitution rate through time, and more flexible relaxed clock models are required for robust inference of rates and dates. Estimation of relaxed molecular clocks using Bayesian Markov chain Monte Carlo is computationally expensive and may not scale well to large datasets. We build on recent advances in maximum likelihood and least-squares phylogenetic and molecular clock dating methods to develop a fast relaxed-clock method based on a Gamma-Poisson mixture model of substitution rates. This method estimates a distinct substitution rate for every lineage in the phylogeny while being scalable to large phylogenies. Unknown lineage sample dates can be estimated as well as unknown root position. 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, treedater.
AU - Volz,EM
AU - Frost,SDW
DO - ve/vex025
PY - 2017///
SN - 2057-1577
TI - Scalable relaxed clock phylogenetic dating
T2 - Virus Evolution
UR - http://dx.doi.org/10.1093/ve/vex025
UR - http://hdl.handle.net/10044/1/50673
VL - 3
ER -