Computational protocol: Evolution of Hepatitis B Virus in a Chronic HBV-Infected Patient over 2 Years

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Protocol publication

[…] Fourteen HBV complete genomes available in GenBank (genotypes A, B and E to H) were applied to phylogenetic analysis. Additionally, 50 published sequences of genotype C were also used in this study for alignment analysis (Genbank accession numbers can be obtained upon request). The whole genome sequences were assembled by BioEdit sequence alignment editor software, version []. Alignment was performed using Clustal X software, version 1.83 []. Phylogenetic and molecular evolutionary analysis of nucleotide differences within and between the isolate sequences were carried out by MEGA program, version 3.1 []. Genetic distance was estimated using the Kimura two-parameter algorithm. The phylogenetic trees were constructed by the neighbor-joining method. Bootstrap re-sampling and reconstruction were carried out for 1,000 times to confirm the reliability of phylogenetic trees. […]

Pipeline specifications

Software tools BioEdit, Clustal W, MEGA
Applications Phylogenetics, WGS analysis
Organisms Hepatitis B virus, Homo sapiens
Diseases Hepatitis B, Infection