bootstrap n-j tree algorithm  (GENETYX CORPORATION)

Journal: Viruses

Article Title: Identification and Long-Term Detection of Hepacivirus bovis Genotype 1 and 2 on a Cattle Farm in Germany

doi: 10.3390/v18010078

Figure Lengend Snippet: Phylogenetic analysis of Hepacivirus bovis (BovHepV). The complete BovHepV genome sequences were aligned using MAFFT. Subsequently, a maximum likelihood analysis was performed using the maximum likelihood method and the Tamura–Nei model, including 1000 bootstrap replicates (Geneious v.11.1.5 software package (Biomatters, New Zealand)). The scale indicates the nucleotide substitutions per site. The BovHepV strains analyzed in this study are marked with a black square. The viruses are labeled with their accession number, virus ID, and country of origin. The genome of the hepatitis GB virus was used as an outgroup. The corresponding genotypes and subtypes were defined on the basis of a previous publication .

Article Snippet: A maximum likelihood analysis was subsequently performed using the maximum likelihood method and the Tamura–Nei model, including 1000 bootstrap replicates (Geneious v.11.1.5 software package (Biomatters, New Zealand)).

Techniques: Software, Labeling, Virus

Journal: Viruses

Article Title: Identification and Long-Term Detection of Hepacivirus bovis Genotype 1 and 2 on a Cattle Farm in Germany

doi: 10.3390/v18010078

Figure Lengend Snippet: Phylogenetic analysis of 55 partial BovHepV-1 sequences of the NS3 gene from the years 2020–2022. The partial BovHepV genome sequences were aligned using MAFFT. Subsequently, a maximum likelihood analysis was performed using the maximum likelihood method and the Tamura–Nei model, including 1000 bootstrap replicates. The scale indicates the nucleotide substitutions per site. The viruses are labeled with their accession number, cattle ID, sampling date, and sample ID. The table on the right summarizes several key observations: (I) different cattle carry genetically identical virus, (II) identical viruses persist for months or years in the same animal, (III) reinfections with novel BovHepV variants, either with alternative subtypes or genetically distinct strains within the same subtype, are possible. The letter–number combination continuously identifies the corresponding animals/samples in a subgroup. Examples of how to interpret the table in the figure are as follows: Column I: The four cattle in subgroup A (A1, A2, A3, and A4) all carry a virus with the identical NS3 gene sequence. Column II: In cattle R885, the identical virus sequence was found in four samples taken between October 2020 and 22 October (M1 to M4 in column II). The accession numbers and sample IDs are also summarized in .

Article Snippet: A maximum likelihood analysis was subsequently performed using the maximum likelihood method and the Tamura–Nei model, including 1000 bootstrap replicates (Geneious v.11.1.5 software package (Biomatters, New Zealand)).

Techniques: Labeling, Sampling, Virus, Sequencing