Selected article for: "beast program and clock model"
Author: Lau, Susanna K. P.; Wong, Antonio C. P.; Lau, Terrence C. K.; Woo, Patrick C. Y.
Title: Molecular Evolution of MERS Coronavirus: Dromedaries as a Recent Intermediate Host or Long-Time Animal Reservoir?
  • Document date: 2017_10_16
    • ID: 1sq2uvur_48
    Snippet: Divergence times for the MERS-CoV strains were calculated using a Bayesian Markov chain Monte Carlo (MCMC) approach implemented in BEAST (version 1.7.4) (BEAST Developers, Open Source, available online: beast.community/programs), as described previously [25, 26] . Representative strains were selected for MERS-CoV strains with close sequence similarity and obtained from the same outbreak. Analyses were performed under the SRD06 substitution models.....
    Document: Divergence times for the MERS-CoV strains were calculated using a Bayesian Markov chain Monte Carlo (MCMC) approach implemented in BEAST (version 1.7.4) (BEAST Developers, Open Source, available online: beast.community/programs), as described previously [25, 26] . Representative strains were selected for MERS-CoV strains with close sequence similarity and obtained from the same outbreak. Analyses were performed under the SRD06 substitution models for the spike coding regions of the genome (S), with an uncorrelated exponential relaxed clock and a constant size coalescent model. The MCMC run was 5 × 10 7 steps long with sampling every 1000 steps. Convergence was assessed on the basis of the effective sampling size after a 10% burn-in using Tracer software, version 1.6.0 (Available online: http://tree.bio.ed.ac.uk/software/tracer/). The mean time to tMRCA and the highest posterior density regions at 95% (HPDs) were calculated. The trees were summarized in a target tree by using the Tree Annotator program included in the BEAST package by choosing the tree with the maximum sum of posterior probabilities (maximum clade credibility) after a 10% burn-in.

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