Computational protocol: Endurance, Refuge, and Reemergence of Dengue Virus Type 2, Puerto Rico, 1986–2007

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Protocol publication

[…] Coding sequences for the unprocessed polyprotein (5′ and 3′ noncoding regions excluded) were aligned by ClustalW software (www.ebi.ac.uk/Tools/clustalw/index.html) in MEGA 4 (www.megasoftware.net). Maximum likelihood analysis and bootstrapping tests were performed in PAUP* () under the best-fit substitution model estimated by MODELTEST v3.07 () (parameters available on request). The 1983 Jamaican isolate JM_83_M20558 () served as outgroup. Mean rates of nucleotide substitution and relative genetic diversity (Net, where t is the generation time) were estimated by using Bayesian Markov Chain Monte Carlo (MCMC) from BEAST v1.4.7 (http://mbe.oxfordjournals.org/content/25/7/1459). General time reversible substitution model with strict and relaxed molecular clocks and constant population size or Bayesian Skyline coalescent analysis was used. All MCMC chains were run for sufficient length ensuring stationary parameters, with statistical error reflected in values of the 95% highest probability density. Amino acid differences were mapped by using parsimony methods in MacClade v4.08 (). We determined dN/dS ratios with the single likelihood ancestor counting method using HYPHY and accessed through the Datamonkey server (). Associations between phylogeny and geographic data were investigated by using Bayesian Tip-association Significance testing (http://evolve.zoo.ox.ac.uk/evolve/BaTS.html) with the posterior sample of trees calculated by BEAST. For the parsimony score, association index, and monophyletic clade size, we considered p<0.05 significant. […]

Pipeline specifications

Software tools Clustal W, MEGA, ModelTest-NG, MacClade, HyPhy, Datamonkey, BaTS
Applications Phylogenetics, Population genetic analysis
Organisms Dengue virus 2