Computational protocol: Subgenotype reclassification of genotype B hepatitis B virus

Similar protocols

Protocol publication

[…] We have previously analyzed a total of 3471 full length genome sequences of HBV using a phylogenetic approach []. Our results showed that 860 sequences belonged to genotype B. These sequences were selected to generate a new dataset for further analysis. In addition, a sequence of genotype C (GenBank:EU939604) was also included in the new dataset and used as an outgroup. Information of these sequences, such as subgenotype and recombination, was also extracted from GenBank annotations. For sequences with a reference available in Pubmed, we performed an extensive literature review to obtain their subgenotype and recombination information. This information was used to define the subgenotypes.Phylogenetic analysis of the genotype B strains was carried out using RAxML [] under the GTRCAT approximation [] and random starting trees. Three thousand rapid bootstrap replicates were performed and all other parameters were set to default. Trees were visualized and analyzed using Dendroscope []. The tree is available as Additional file .The mean nucleotide divergence (mean ± SD) between different subgenotypes was calculated using Mega 5 [] under the Kimura 2-parameter model []. Five hundred bootstrap replicates were applied to obtain consistent and reliable sequence divergence values. […]

Pipeline specifications

Software tools RAxML, Dendroscope, MEGA
Application Phylogenetics
Organisms Hepatitis B virus
Diseases Hepatitis B