Imperial College London


Faculty of MedicineSchool of Public Health

Senior Lecturer



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




UG10Norfolk PlaceSt Mary's Campus






BibTex format

author = {Siveroni, IA and Volz, EM},
title = {PhyDyn: Epidemiological Modelling in BEAST},
type = {Software},
year = {2017}

RIS format (EndNote, RefMan)

AB - PhyDyn is a BEAST2 package for performing Bayesian phylogenetic inference under models that deal with structured populations with complex population dynamics. This package enables simultaneous estimation of epidemiological parameters and pathogen phylogenies.PhyDyn implements a structured coalescent model for a large class of epidemic processes specified by a deterministic nonlinear dynamical system, and computes the log-likelihood of a gene genealogy conditional on a complex demographic history. Genealogies are specified as timed phylogenetic trees in which lineages are associated with the distinct subpopulation in which they are sampled. Epidemic models are defined by a series of ordinary differential equations (ODEs) specifying the rates that new lineages introduced in the population (birth matrix) and the rates at which migrations, or transition between states occur (migration matrix).
AU - Siveroni,IA
AU - Volz,EM
PY - 2017///
TI - PhyDyn: Epidemiological Modelling in BEAST
ER -