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Bioedit Company 1000 replicates bootstrap
1000 Replicates Bootstrap, supplied by Bioedit Company, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Article Title: Genome-wide characterization of Histone gene family and expression profiling during microspore development in radish (Raphanus sativus L.).
Article Snippet: Histone, a predominant protein component of chromatin, participates in DNA packaging and transcriptional regulation.. However, the available information of Histone gene family is limited in radish.. In this study, a total of 42 Histone gene family members were identified from the radish genome.

Article Title: Identifying the Viral Genes Encoding Envelope Glycoproteins for Differentiation of Cyprinid herpesvirus 3 Isolates
Article Snippet: Also, the phylogenetic analysis was conducted using Bioedit software and Molecular Evolutionary Genetics Analysis (MEGA) 5 software, with bootstrap values calculated from 1000 replicates.

Article Title: Identification and Functional Analysis of the G1 Phase Cyclin Dependent Kinase Gene Hc-CDK6 in Pearl Mussels (Hyriopsis cumingii)
Article Snippet: Multiple comparisons of amino acid sequences and phylogenetic tree construction (neighbor-joining method, 1000 bootstrap replicates) were performed in Bioedit and MEGA7.0, respectively.

Article Title: Molecular characterization of Sweet potato feathery mottle virus and sweet potato yield loss due to its infection
Article Snippet: Nucleotide homology levels were analyzed with BioEdit software, while the phylogenetic tree was analyzed with Molecular Evolutionary Genetic Analysis (MEGA v6.0) software using the neighbor-joining method with 1000 times bootstrap.

Article Title: Genome-wide analyses of histone modifications and chromatin accessibility reveal the distinct genomic compartments in the Irish potato famine pathogen Phytophthora infestans
Article Snippet: Sequence alignment was performed by Bioedit software [ ], and phylogenetic analysis was conducted by MEGA5 using neighbor- joining model and 10000 bootstrap replicates [ ].

Article Title: Pathogenicity of H5N8 highly pathogenic avian influenza viruses isolated from a wild bird fecal specimen and a chicken in Japan in 2014.
Article Snippet: Phylogenetic analysis of the sequences was performed using BioEdit software (46) andMEGA 5.2 software (47) by the neighbor-joining method with a bootstrap test of 1000 replicates.

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Article Title: Identification of the bacteria associated to the phycosphere of the Chlorella-like strain SEC_LI_ChL_1
Article Snippet: The associations and the co-evolution of bacteria and eukaryotic microalgae are raising great interest in the last years, especially in the “phycosphere”, that is the area around the algal cells, where extracellular products of the algae are used by bacteria; here, different interactions between microalgae and bacteria might occur.. The Chlorella-like strain SEC_LI_ChL_1 was previously characterized with a multidisciplinary integrated approach based on phylogenetic reconstructions, morphological-ultrastructural analysis and physiological characterization in presence of different trophic conditions.. In this work, the isolation and characterization of fifteen cultivable and one uncultivable bacterial strains strictly associated to the phycosphere of strain SEC_LI_ChL_1 was carried out.



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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 <t>the</t> <t>Tamura–Nei</t> model, including <t>1000</t> 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 .
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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 .

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

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 .

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