CoaTran

CoaTran simulates coalescent viral phylogenies constrained by user-provided transmission networks and sample times to support molecular epidemiology analyses.

Key Features:

• Massively Scalable Simulations: Implements global population-scale phylogenetic coalescent simulations in a highly-optimized C++ codebase, enabling large-scale runs that complete in seconds to minutes.
• Transmission Network Constraints: Accepts transmission networks and sample times as inputs and enforces those constraints so simulated phylogenies are consistent with specified transmission histories.
• Benchmarking and Insight Generation: Produces simulated datasets suitable for benchmarking computational tools in molecular epidemiology and for exploring unobservable virological characteristics of novel pathogens.

Scientific Applications:

• Molecular Epidemiology Benchmarking: Generates constrained coalescent phylogenies for evaluation and validation of phylogenetic and phylodynamic methods.
• Outbreak Modeling and Intervention Assessment: Enables simulation of transmission-linked evolutionary scenarios to model outbreak dynamics and assess potential intervention strategies.

Methodology:

CoaTran takes transmission networks and sample times as inputs and simulates the coalescent process constrained by those networks, implemented in an optimized C++ codebase for scalability.