Computational protocol: Characterization of the Copy Number and Variants of Deformed Wing Virus (DWV) in the Pairs of Honey Bee Pupa and Infesting Varroa destructor or Tropilaelaps mercedesae

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Protocol publication

[…] Prior to phylogenetic analysis, we aligned nucleotide sequences using Mafft (v7.307) () and then used Gblocks (v0.91b) () to automatically eliminate divergent regions or gaps. The best fit nucleotide substitution models were determined for the alignments by Jmodeltest (v2.1.10) with parameters set to “-g 4 -i -f -AIC -BIC -a” (). Mrbayes (v3.2.3) () was run with the parameters set to 1,000,000 (1 sample/100 generations) until split frequencies were below 0.01. The first 25% of samples for each run were designated as the burn-in. DWV type A strain (NC_004830.2), DWV type B strain (NC_006494.1), DWV type C strain (CEND01000001.1), and Sacbrood virus (NC_002066.1) were used as references. […]

Pipeline specifications

Software tools MAFFT, Gblocks, jModelTest, MrBayes
Application Phylogenetics
Organisms Apis mellifera, Deformed wing virus, Varroa destructor