Computational protocol: Spatiotemporal Characterizations of Dengue Virus in Mainland China: Insights into the Whole Genome from 1978 to 2011

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Protocol publication

[…] Phylogenetic analysis was performed on a gene-by-gene basis using the sequences of the coding region and the non-coding region of 40 DENV strains isolated in mainland China. Sequence alignments were performed using the Clustal W program, which resulted in alignments of the complete sequence and for each individual gene sequence for each of the four DENV serotypes. Maximum likelihood (ML) phylogenetic trees were then estimated using the MEGA (Molecular Evolutionary Genetics Analysis) 5.05 software. To determine the support for a particular grouping on the phylogenetic trees, bootstrap re-sampling analyses was performed using 1000 replicate neighbor-joining trees estimated by using the ML substitution model. [...] All the DENV-1 and DENV-2 isolates were analyzed using “DataMonkey” (available online: http://www.datamonkey.org/). The recombination events of the dengue viruses were analyzed using the genetic algorithm (GARD). The GARD method for detecting recombination was demonstrated in a previous study . The neighbor-joining trees between the breakpoints were also demonstrated. […]

Pipeline specifications

Software tools Clustal W, MEGA, Datamonkey, GARD
Applications Phylogenetics, Population genetic analysis
Diseases HIV Infections