Contagion is a new type of forward genetic simulator and disease outbreak simulator specially designed to explicitly model evolution both within- and between-host scales of reference simultaneously. At the within-host level, Contagion simulates the processes of replication, mutation, selection, and drift on viral pathogen sequences. At the host population level, Contagion performs like an epidemic simulator that tracks the infection status of individual hosts and simulates pathogen transmission between hosts conditioned on the available routes present in a given host population.
Contagion is currently under development and APIs may change.
If encounter problems or have questions or feature requests, please feel contact me -
Kent Kawashima
Email: kentkawashima@nig.ac.jp
Twitter: @kent
Apache License, Version 2.0 Copyright 2018 Kent Kawashima