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2.5. Clustering analyses and phylogenetic tree construction

XY Xiaowen Yang
DP Dongri Piao
LM Lingling Mao
BP Bo Pang
HZ Hongyan Zhao
GT Guozhong Tian
HJ Hai Jiang
BK Biao Kan
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One genome that had the highest coverage for all isolates was selected as the reference. PhyloSNP [22] was used to generate phylogenetic trees. The neighbour-joining (NJ) method with 1000 bootstraps was used.

SNP matrix data were also analyzed using phyloSNP. A minimum spanning (MS) tree was generated with BioNumerics software (http://www.applied-maths.com/bionumerics) using default software settings. The links between the MS tree nodes represented the distance between the genotypes. The cluster cutoff value was defined as the maximum pairwise distance found between epidemiologically linked isolates.

Copyright and License information:  ©2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group, on behalf of Shanghai Shangyixun Cultural Communication Co., Ltd
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 use, distribution, and reproduction in any medium, provided the original work is properly cited.

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