Computational protocol: Structural, Antigenic, and Evolutionary Characterizations of the Envelope Protein of Newly Emerging Duck Tembusu Virus

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Protocol publication

[…] MEGA5 was used to find optimal nucleotide substitution model. The TN93+G (Hasegawa-Kishino-Yano) model was predicted to be the best to describe the substitution patterns for the nucleotide sequences of E genes. Six complete sequences of DTMUV E genes described in this study and other fifteen complete E sequences reported previously , , , , , with total 21 were used in this study. Viruses that derived these E genes were obtained from diseased meat and laying ducks in affected areas during epidemics spanning 2010–2012. The phylogenetic tree and evolutionary rate were inferred using Bayesian method in Beast (http://beast.bio.ed.ac.uk/Main_Page). Lognormal relaxed uncorrelated molecular clock model was chosen to estimate evolutionary rate; the tree prior was set to a constant size coalescent; the evolutionary rate was calculated separately for the three-codon positions; a uniform distribution was specified as a prior for relative mutation rate sampling. To achieve convergence and derive sufficient effective sample size (>300), 5×108 Markov Chain Monte Carlo iterations were run and trees were sampled every 2000 iterations. The first 10% trees were used as burn-in for tree construction and parameter estimation. Evolutionary rate and divergence time were estimated using Tracer (http://beast.bio.ed.ac.uk/Tracer). Maximum clade credibility trees were constructed using TreeAnnotator and viewed in FigTree (http://beast.bio.ed.ac.uk/FigTree). […]

Pipeline specifications

Software tools MEGA, BEAST, FigTree
Application Phylogenetics
Organisms Anas platyrhynchos, Tembusu virus, Japanese encephalitis virus
Diseases Encephalitis