CoaTran: Coalescent tree simulation along a transmission network

MotivationThe 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. ResultsCoaTran 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. AvailabilityCoaTran is freely available at https://github.com/niemasd/CoaTran as an open-source software project. Contactniema@ucsd.edu Supplementary informationSupplementary data are available online.