Summary
In epidemiology of infectious diseases, networks have been used to reconstruct contacts among patients. Summarizing networks using pathogen metadata (e.g., host species and place of isolation) and a phylogenetic tree is a nascent 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 derived from networks and metrics. We created a web-based application, called StrainHub, in which a user can input a phylogenetic tree along with characters derived from metadata using their preferred tree search method. StrainHub generates a transmission network for the user metadata based on character state changes 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, 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.
Availability https://github.com/abschneider/StrainHub and strainhub.io
