Selected article for: "clock model and MCMC chain"
Author: Adrian Egli; Nina Goldman; Nicola F. Müller; Myrta Brunner; Daniel Wüthrich; Sarah Tschudin-Sutter; Emma Hodcroft; Richard Neher; Claudia Saalfrank; James Hadfield; Trevor Bedford; Mohammedyaseen Syedbasha; Thomas Vogel; Noémie Augustin; Jan Bauer; Nadine Sailer; Nadezhda Amar-Sliwa; Daniela Lang; Helena M.B. Seth-Smith; Annette Blaich; Yvonne Hollenstein; Olivier Dubuis; Michael Nägele; Andreas Buser; Christian H. Nickel; Nicole Ritz; Andreas Zeller; Tanja Stadler; Manuel Battegay; Rita Schneider-Sliwa
Title: High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters
  • Document date: 2020_4_4
    • ID: n57hoty4_71
    Snippet: Phylogenetic trees of initial clusters. We next estimated rates of evolution for each segment using 741 the SRD06 model 60 and a strict clock model, from 200 full genome sequences sampled in 742 California, New York and Europe between 2010 and 2015, using Beast 2.5 61 . Apart from this, 743 these sequences were not otherwise used in the analysis, and as such are an independent 744 dataset. We allowed each segment to have its own phylogeny in orde.....
    Document: Phylogenetic trees of initial clusters. We next estimated rates of evolution for each segment using 741 the SRD06 model 60 and a strict clock model, from 200 full genome sequences sampled in 742 California, New York and Europe between 2010 and 2015, using Beast 2.5 61 . Apart from this, 743 these sequences were not otherwise used in the analysis, and as such are an independent 744 dataset. We allowed each segment to have its own phylogeny in order to avoid the possibility of 745 a reassortment biasing the estimates of evolutionary rates. Each of the segments, as well as the 746 first two and third codon position was allowed to have its own rate scaler. We ran ten independent 747 Markov Chain Monte Carlo (MCMC) chains each for 10 8 iterations and then combined them after 748 a burn-in of 10%. These estimated evolutionary rates are long-term rates of influenza A/H3N2.

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