Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.11.10.377499v1?rss=1

Authors: Moshiri, N.

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.

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