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FAVITES (FrAmework for VIral Transmission and Evolution Simulation) is a robust modular framework for the simultaneous simulation of a transmission network and viral evolution, as well as simulation of sampling imperfections of the transmission network and of the sequencing process. The framework is robust in that the simulation process has been broken down into a series of interactions between abstract module classes, and the user can simply plug in each desired module implementation (or implement one from scratch) to customize any stage of the simulation process.

Contents

• Installation
• Usage
• Output Folder Structure
• Designing a Configuration File
• Post-Validation
• Network Visualization
• General Workflow
• File Formats
• Modules
• Development Guide

Network Visualization

FAVITES outputs the transmission network in two formats: the FAVITES format and the GEXF format. To visualize the transmission network, we recommend opening the GEXF transmission network in Gephi, a popular cross-platform open-source tool. The GEXF transmission network FAVITES outputs is a dynamic network, meaning you can use Gephi to visualize the growth of the transmission network over time.

In the GEXF file, each node is given a single attribute, "infected," which is set to false at time 0 and is set to true upon infection, and each edge is given a single attribute, "transmission," which is set to false at time 0 and is set to true upon a transmission event along that edge. Simply load the GEXF file outputted by FAVITES in Gephi, go to the "Appearance" box, go to the "Nodes" tab to set the desired colors for infected and uninfected (which would be "true" and "false" for the "infected" attribute, respectively), go to the "Edges" tab to set the desired colors for transmission edges and normal contact network edges (which would be "true" and "false" for the "transmission" attribute, respectively), and set "Enable auto transformation - applied continuously" to have the colors change automatically in the timeline view.