Selected article for: "data set and Methods Materials"
Author: Chan, Joseph M.; Rabadan, Raul
Title: Quantifying Pathogen Surveillance Using Temporal Genomic Data
  • Document date: 2013_1_29
    • ID: u2t1x89m_23
    Snippet: To determine the impact of site and clock rate heterogeneity in quantifying surveillance completeness, we calculated the p2 coefficient of the human H5N1 HA data set of 158 sequences by using BEAST (see Materials and Methods). We accounted for site heterogeneity by using the gamma model (39) and reconstructed trees under both strict and relaxed molecular clocks. We calculated the p2 coefficients to be 0.848 (0.740 to 0.917) and 0.860 (0.721 to 0......
    Document: To determine the impact of site and clock rate heterogeneity in quantifying surveillance completeness, we calculated the p2 coefficient of the human H5N1 HA data set of 158 sequences by using BEAST (see Materials and Methods). We accounted for site heterogeneity by using the gamma model (39) and reconstructed trees under both strict and relaxed molecular clocks. We calculated the p2 coefficients to be 0.848 (0.740 to 0.917) and 0.860 (0.721 to 0.911) for the strict and relaxed clocks, respectively. Given our q2 coefficient of 0.821 (0.795 to 0.848) for human H5N1 HA, we concluded that incorporating site heterogeneity and a relaxed molecular clock did not make a significant difference.

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