Computational protocol: A dengue outbreak on a floating village at Cat Ba Island in Vietnam

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Protocol publication

[…] E gene sequences were aligned using MUSCLE v.3.8.31 []. The maximum likelihood (ML) phylogenetic trees were inferred with RAxML (Randomized Axelerated Maximum Likelihood) v. 8.1.17 []. GTR + Γ + I was selected as the nucleotide substitution model using jModeltest v.2.1.7 []. The statistical robustness and reliability of each node was assessed with 1000 bootstrap replicates. FigTree v.1.4.2 [] was used to visualize the inferred ML tree. […]

Pipeline specifications

Software tools MUSCLE, RAxML, jModelTest, FigTree
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Homo sapiens
Diseases Dengue, Infection