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Niema Moshiri edited this page Apr 16, 2018 · 96 revisions

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.

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Helper Scripts and Post-Validation

In addition to the main FAVITES workflow, we have included numerous tools that may be helpful for running FAVITES and interpreting the results. We have a series of Helper Scripts that perform various basic miscellaneous tasks (e.g. converting between filetypes, computing interpretable statistics on files, etc.) as well as a series of Post-Validation tools that allow you to gauge how realistic your simulated output looks (e.g. comparing simulated phylogenetic trees against a realistic tree, comparing simulated sequence data against real sequences, etc.).

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.