Selected article for: "host tree and virus host"
Author: Geoghegan, Jemma L.; Duchêne, Sebastián; Holmes, Edward C.
Title: Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families
  • Document date: 2017_2_8
    • ID: 1u44tdrj_31
    Snippet: We measured the extent of virus-host co-divergence (and by exclusion host-jumping) by comparing, in a quantitative manner, the tree topologies for viruses and their corresponding hosts. To this end we calculated a normalized PH85 tree topological distance [14] , referred to here as the 'nPH85' distance (this function has been included in NELSI v0.1 [45] ). Specifically, the nPH85 distance, which utilizes two phylogenetic trees as its input, descr.....
    Document: We measured the extent of virus-host co-divergence (and by exclusion host-jumping) by comparing, in a quantitative manner, the tree topologies for viruses and their corresponding hosts. To this end we calculated a normalized PH85 tree topological distance [14] , referred to here as the 'nPH85' distance (this function has been included in NELSI v0.1 [45] ). Specifically, the nPH85 distance, which utilizes two phylogenetic trees as its input, describes the number of bipartitions (clades) that are not shared between two tree topologies. Importantly, it does not depend on the nodes where the topological differences occur in the tree (Fig 1) . In addition, this metric considers the tree topology of unrooted trees, but not the branch lengths of the tree. First, the PH85 metric is calculated as the topological distance between a pair of unrooted trees. It can be understood in terms of the following:

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