Abstract
Motivation The ability to simulate coalescent viral phylogenies constrained by a given transmission network can enable the benchmarking of computational tools used in molecular epidemiology as well as the ability to gain insights into unobservable aspects of the virology of a novel pathogen. However, such simulation experiments require generating a large number of technical simulation replicates, and existing tools for coalescent simulations along a transmission network are too slow to conduct such experiments at the scale of the global population.
Results CoaTran is a massively scalable tool that simulates a coalescent viral phylogeny constrained by a user-provided transmission network. CoaTran is written in highly-optimized C++ code and can generate global population scale phylogenetic coalescent simulations in seconds to minutes.
Availability CoaTran is freely available at https://github.com/niemasd/CoaTran as an open-source software project.
Contact niema{at}ucsd.edu
Supplementary information Supplementary data are available online.
Competing Interest Statement
The authors have declared no competing interest.
