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Bioinformatics. 2019 Aug 16. pii: btz646. doi: 10.1093/bioinformatics/btz646. [Epub ahead of print]

StrainHub: A phylogenetic tool to construct pathogen transmission networks.

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Department of Medicine, University of California San Diego, San Diego, United States of America.
Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, United States of America.
School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, United States of America.



In exploring the epidemiology of infectious diseases, networks have been used to reconstruct contacts among individuals and/or populations. Summarizing networks using pathogen metadata (e.g., host species and place of isolation) and a phylogenetic tree is a nascent, alternative approach. In this paper, we introduce a tool for reconstructing transmission networks in arbitrary space from phylogenetic information and metadata. Our goals are to provide a means of deriving new insights and infection control strategies based on the dynamics of the pathogen lineages derived from networks and centrality metrics. We created a web-based application, called StrainHub, in which a user can input a phylogenetic tree based on genetic or other data along with characters derived from metadata using their preferred tree search method. StrainHub generates a transmission network based on character state changes in metadata, such as place or source of isolation, mapped on the phylogenetic tree. The user has the option to calculate centrality metrics on the nodes including betweenness, closeness, degree, and a new metric, the source/hub ratio. The outputs include the network with values for metrics on its nodes and the tree with characters reconstructed. All of these results can be exported for further analysis.


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