CoaTran: Coalescent tree simulation along a transmission network

Published in bioRxiv, 2020

Recommended citation: Moshiri N (2020). "CoaTran: Coalescent tree simulation along a transmission network." bioRxiv. doi:10.1101/2020.11.10.377499


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.


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.


CoaTran is freely available at as an open-source software project.