Computational protocol: Enterovirus D68 Infections Associated with Severe Respiratory Illness in Elderly Patients and Emergence of a Novel Clade in Hong Kong

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Protocol publication

[…] The number of synonymous substitutions per synonymous site, dS, and non-synonymous substitutions per non-synonymous site, dN, in VP1 were calculated using Nei-Gojobori method (Jukes-Cantor) in MEGA5. Sites under positive selection were inferred using single-likelihood ancestor counting (SLAC) and fixed effects likelihood (FEL) methods as implemented in DataMonkey server ( The overall ω (dN/dS) value was calculated according to NJ trees under the TrN93 substitution model. Positive selection for a site was considered to be statistically significant if P-value was <0.1. A mixed-effects model of evolution (MEME) was further used to identify positively selected sites under episodic diversifying selection in particular positions among different clades within a phylogenetic tree even when positive selection is not evident across the entire tree. The relative residue abundance within BC and DE-surface exposed loops were depicted using WebLogo. […]

Pipeline specifications

Software tools Datamonkey, WebLogo
Applications Phylogenetics, Population genetic analysis, Genome data visualization
Organisms Homo sapiens
Diseases Enterovirus Infections, Pneumonia, Respiratory Insufficiency
Chemicals Amino Acids