Author: Gytis Dudas; Luiz Max Carvalho; Andrew Rambaut; Trevor Bedford; Ali M. Somily; Mazin Barry; Sarah S. Al Subaie; Abdulaziz A. BinSaeed; Fahad A. Alzamil; Waleed Zaher; Theeb Al Qahtani; Khaldoon Al Jerian; Scott J.N. McNabb; Imad A. Al-Jahdali; Ahmed M. Alotaibi; Nahid A. Batarfi; Matthew Cotten; Simon J. Watson; Spela Binter; Paul Kellam
Title: MERS-CoV spillover at the camel-human interface Document date: 2017_8_10
ID: 8xcplab3_57
Snippet: To ensure that recombination was not interfering with the skygrid reconstruction we also split our MERS-CoV alignment into ten parts 2937 nucleotides long. These were then used as separate partitions with independent trees and clock rates in BEAST v1.8.4 (Drummond et al., 2012) . Nucleotide substitution and relaxed clock models were set up identically to the whole genome skygrid analysis described above (Drummond et al., 2006; Hasegawa et al., 19.....
Document: To ensure that recombination was not interfering with the skygrid reconstruction we also split our MERS-CoV alignment into ten parts 2937 nucleotides long. These were then used as separate partitions with independent trees and clock rates in BEAST v1.8.4 (Drummond et al., 2012) . Nucleotide substitution and relaxed clock models were set up identically to the whole genome skygrid analysis described above (Drummond et al., 2006; Hasegawa et al., 1985; Yang, 1994) . Skygrid coalescent tree prior (Gill et al., 2013) was used jointly across all ten partitions for demographic inference. Five MCMC chains were set up, each running for 200 million states, sampling every 20 000 states.
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