PT - JOURNAL ARTICLE AU - Moshiri, Niema TI - CoaTran: Coalescent tree simulation along a transmission network AID - 10.1101/2020.11.10.377499 DP - 2020 Jan 01 TA - bioRxiv PG - 2020.11.10.377499 4099 - http://biorxiv.org/content/early/2020/11/11/2020.11.10.377499.short 4100 - http://biorxiv.org/content/early/2020/11/11/2020.11.10.377499.full AB - 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.eduSupplementary information Supplementary data are available online.Competing Interest StatementThe authors have declared no competing interest.