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. 2018 Jul 12;8:10552. doi: 10.1038/s41598-018-28908-7

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© The Author(s) 2018

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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A comparison of clades identified by maximum likelihood via the SNVPhyl pipeline and by network analysis. The orientation of clades and divergent single strains are identified by brackets in the maximum likelihood phylogenetic tree (left) and clusters are identified by red circles in the network analysis (right). The numbers identify the clades and corresponding clusters.