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. 2016 Sep 11;66(1):e66–e82. doi: 10.1093/sysbio/syw077

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© The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 2. — An example of a transmission process simulated under a parameter configuration without subsampling of the simulated infectious population. Arrows indicate the sequence of random events taking place in the simulation and different colors represent different haplotypes of the pathogen. The simulation starts with one infectious host who transmits the pathogen to another host. After one more transmission event, the pathogen undergoes a mutation within one of the three hosts infected so far (event three). As the sixth event in the simulation, one of the haplotypes is removed from the population due to the recovery/death of the corresponding host. The simulation stops when the infectious population size exceeds and the simulator outputs the generated . The nodes not connected by arrows show all the other possible configurations of the infectious population, but which were not visited in this example run of the simulator. The bottom row lists the possible outputs of the simulator (cluster size vectors) under their corresponding population configuration.

Inline graphic — An example of a transmission process simulated under a parameter configuration without subsampling of the simulated infectious population. Arrows indicate the sequence of random events taking place in the simulation and different colors represent different haplotypes of the pathogen. The simulation starts with one infectious host who transmits the pathogen to another host. After one more transmission event, the pathogen undergoes a mutation within one of the three hosts infected so far (event three). As the sixth event in the simulation, one of the haplotypes is removed from the population due to the recovery/death of the corresponding host. The simulation stops when the infectious population size exceeds and the simulator outputs the generated . The nodes not connected by arrows show all the other possible configurations of the infectious population, but which were not visited in this example run of the simulator. The bottom row lists the possible outputs of the simulator (cluster size vectors) under their corresponding population configuration.

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