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. 2018 Sep 5;15(146):20180512. doi: 10.1098/rsif.2018.0512

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© 2018 The Authors.

Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

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Figure 1. — Visual representation of the phylogeny under an MSBD model. Each state is represented by a colour: the ancestral state, in black, starts at the root and represent the first transmission cluster. The other states, in blue, red and green, start at change points along the tree. These states represent further transmission clusters in the course of the epidemic, and the state change points represent the introduction of the pathogen into a new community. Here t_c, t_t and t_s are the times of, respectively, a state change, transmission and sampling event, as they appear in equation (2.2).