Computational protocol: Low Prevalence of Rotavirus and High Prevalence of Norovirus in Hospital and Community Wastewater after Introduction of Rotavirus Vaccine in Nicaragua

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Protocol publication

[…] Sequence alignment of the Nicaraguan strains and reference NoV genotypes representing known genotypes as well as GII.4 variants, was performed by using the ClustalW algorithm, version 2, at the European Bioinformatics Institute server (EMBL-EBI). Phylogenetic analysis was performed using the MEGA 5.0 software package, and the tree was constructed using the neighbor-joining and Kimura two parameter methods. Significance of the relationship was obtained by bootstrap re-sampling analysis (1,000 replications). […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Bos taurus, Homo sapiens
Diseases Rotavirus Infections