Computational protocol: Recombination in West Nile Virus: minimal contribution to genomic diversity

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Protocol publication

[…] To look for recombination in WNV isolates, we used 154 whole genome Kunjin virus and West Nile virus sequences (See additional file for the original data used) obtained from the Viral Bioinformatics Resource Center . A multiple sequence alignment (MSA) of these genomes was constructed using MUSCLE []. Phylogenetic reconstruction of all available genomic sequences was performed using Bayesian analysis as implemented by the program MrBayes []. We used the default parameters in MrBayes (General Time Reversible evolutionary model, gamma-distributed rate variation and proportion of invariable sites) and sampled every 100 generations for 1 million generations using 4 chains. The first 2,500 trees were discarded as "burn-in". [...] For detection of recombination events, we used the automated suite of algorithms contained within the Recombination Detection Program 3 (RDP3) [,-] to analyze the complete genomic sequences present in our MSA. In general, we used the default settings for each program in the RDP3 suite except for the following: for RDP we used a window size of 30; Bootscan used a window size of 200, step size of 50, and 50 bootstrap replicates; Siscan used a window size of 200 and step size of 20; and RDP3 was set to report all hits detected by 2 or more algorithms. In order to confirm the results from the automated tests, additional algorithms which are not part of the automated process were also run. SplitsTree4 [] was used with default settings to assess the presence of a reticulated phylogenetic network as a representation of recombination (unpublished data). […]

Pipeline specifications

Software tools MUSCLE, MrBayes, RDP4, SplitsTree
Databases VBRC
Applications Phylogenetics, Nucleotide sequence alignment
Organisms West Nile virus
Diseases HIV Infections