Computational protocol: Molecular evolution and the global reemergence of enterovirus D68 by genome-wide analysis

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Protocol publication

[…] A total of 147 full and 1248 partial sequences of EV-D68 were collected for analysis. These sequences were aligned using Clustal Omega version 1.2[] to explore indels in the VP1 gene, with special attention paid to those in Taiwan. To investigate the molecular phylogeny of strains circulating globally, phylogenetic trees were generated using Bayesian Evolutionary Analysis Sampling Trees 2 package[] on VP1 sequences from strains collected in Taiwan, the United States, China, Japan, Mexico, Canada, France, New Zealand, and Haiti. A maximum clade credibility (MCC) tree under the Hasegawa–Kishino–Yano model was estimated. Thirty million Markov chain Monte Carlo chains with 10% burn-in were generated. One MCC tree was constructed for every 3000 chains, and a single consensus tree was summarized from these MCC trees. In addition, all position-specific polymorphisms and substitutions identified by sequence analysis were plotted on graphs using WebLogo 3.[] […]

Pipeline specifications

Software tools Clustal Omega, WebLogo
Applications Phylogenetics, Genome data visualization
Organisms Homo sapiens
Diseases Lymphoma, T-Cell
Chemicals Amino Acids, Nucleotides