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bootscan method  (Simplot Science)

 
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    Simplot Science bootscan method
    Bootscan Method, supplied by Simplot Science, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Genetic characterization of avian HEV. (A) Phylogenetic analysis based on the complete nucleotide sequences of ORF1, ORF2, and ORF3 of avian HEV and reference HEV isolates. Phylogenetic tree constructed using the maximum likelihood (ML) method in PhyML v3.0, under the GTR+Γ+I model. The analysis includes 1000 replicates of the alignment, with bootstrap values indicated at nodes (>70% shown). The red dot denotes the sequence determined in this study. (B) Recombination within the genome of avian HEV strain GDZQ122. <t>Bootscan</t> analysis of the complete genome sequence of avian HEV strain GDZQ122 was conducted using SimPlot program. Parameters: 200 bp window size, 20 bp step size, GapStrip: On, 100 replicates, Kimura (2-parameter), and a T/t ratio of 2.0 in Neighbor-Joining analysis. The phylogenetic trees reconstructed based on three regions of the genome (1–1846, 1847–3014, and 3015–6610) using the maximum likelihood (ML) method in PhyML v3.0 under the best-fit substitution model.
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    Genetic characterization of avian HEV. (A) Phylogenetic analysis based on the complete nucleotide sequences of ORF1, ORF2, and ORF3 of avian HEV and reference HEV isolates. Phylogenetic tree constructed using the maximum likelihood (ML) method in PhyML v3.0, under the GTR+Γ+I model. The analysis includes 1000 replicates of the alignment, with bootstrap values indicated at nodes (>70% shown). The red dot denotes the sequence determined in this study. (B) Recombination within the genome of avian HEV strain GDZQ122. <t>Bootscan</t> analysis of the complete genome sequence of avian HEV strain GDZQ122 was conducted using SimPlot program. Parameters: 200 bp window size, 20 bp step size, GapStrip: On, 100 replicates, Kimura (2-parameter), and a T/t ratio of 2.0 in Neighbor-Joining analysis. The phylogenetic trees reconstructed based on three regions of the genome (1–1846, 1847–3014, and 3015–6610) using the maximum likelihood (ML) method in PhyML v3.0 under the best-fit substitution model.
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    Genetic characterization of avian HEV. (A) Phylogenetic analysis based on the complete nucleotide sequences of ORF1, ORF2, and ORF3 of avian HEV and reference HEV isolates. Phylogenetic tree constructed using the maximum likelihood (ML) method in PhyML v3.0, under the GTR+Γ+I model. The analysis includes 1000 replicates of the alignment, with bootstrap values indicated at nodes (>70% shown). The red dot denotes the sequence determined in this study. (B) Recombination within the genome of avian HEV strain GDZQ122. <t>Bootscan</t> analysis of the complete genome sequence of avian HEV strain GDZQ122 was conducted using SimPlot program. Parameters: 200 bp window size, 20 bp step size, GapStrip: On, 100 replicates, Kimura (2-parameter), and a T/t ratio of 2.0 in Neighbor-Joining analysis. The phylogenetic trees reconstructed based on three regions of the genome (1–1846, 1847–3014, and 3015–6610) using the maximum likelihood (ML) method in PhyML v3.0 under the best-fit substitution model.
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    Genetic characterization of avian HEV. (A) Phylogenetic analysis based on the complete nucleotide sequences of ORF1, ORF2, and ORF3 of avian HEV and reference HEV isolates. Phylogenetic tree constructed using the maximum likelihood (ML) method in PhyML v3.0, under the GTR+Γ+I model. The analysis includes 1000 replicates of the alignment, with bootstrap values indicated at nodes (>70% shown). The red dot denotes the sequence determined in this study. (B) Recombination within the genome of avian HEV strain GDZQ122. <t>Bootscan</t> analysis of the complete genome sequence of avian HEV strain GDZQ122 was conducted using SimPlot program. Parameters: 200 bp window size, 20 bp step size, GapStrip: On, 100 replicates, Kimura (2-parameter), and a T/t ratio of 2.0 in Neighbor-Joining analysis. The phylogenetic trees reconstructed based on three regions of the genome (1–1846, 1847–3014, and 3015–6610) using the maximum likelihood (ML) method in PhyML v3.0 under the best-fit substitution model.
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    Genetic characterization of avian HEV. (A) Phylogenetic analysis based on the complete nucleotide sequences of ORF1, ORF2, and ORF3 of avian HEV and reference HEV isolates. Phylogenetic tree constructed using the maximum likelihood (ML) method in PhyML v3.0, under the GTR+Γ+I model. The analysis includes 1000 replicates of the alignment, with bootstrap values indicated at nodes (>70% shown). The red dot denotes the sequence determined in this study. (B) Recombination within the genome of avian HEV strain GDZQ122. <t>Bootscan</t> analysis of the complete genome sequence of avian HEV strain GDZQ122 was conducted using SimPlot program. Parameters: 200 bp window size, 20 bp step size, GapStrip: On, 100 replicates, Kimura (2-parameter), and a T/t ratio of 2.0 in Neighbor-Joining analysis. The phylogenetic trees reconstructed based on three regions of the genome (1–1846, 1847–3014, and 3015–6610) using the maximum likelihood (ML) method in PhyML v3.0 under the best-fit substitution model.
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    bootscanning method implemented in simplot v3.5.1 program  (Simplot Science)
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    Simplot Science bootscanning method implemented in simplot v3.5.1 program
    Genetic characterization of avian HEV. (A) Phylogenetic analysis based on the complete nucleotide sequences of ORF1, ORF2, and ORF3 of avian HEV and reference HEV isolates. Phylogenetic tree constructed using the maximum likelihood (ML) method in PhyML v3.0, under the GTR+Γ+I model. The analysis includes 1000 replicates of the alignment, with bootstrap values indicated at nodes (>70% shown). The red dot denotes the sequence determined in this study. (B) Recombination within the genome of avian HEV strain GDZQ122. <t>Bootscan</t> analysis of the complete genome sequence of avian HEV strain GDZQ122 was conducted using SimPlot program. Parameters: 200 bp window size, 20 bp step size, GapStrip: On, 100 replicates, Kimura (2-parameter), and a T/t ratio of 2.0 in Neighbor-Joining analysis. The phylogenetic trees reconstructed based on three regions of the genome (1–1846, 1847–3014, and 3015–6610) using the maximum likelihood (ML) method in PhyML v3.0 under the best-fit substitution model.
    Bootscanning Method Implemented In Simplot V3.5.1 Program, supplied by Simplot Science, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Genetic characterization of avian HEV. (A) Phylogenetic analysis based on the complete nucleotide sequences of ORF1, ORF2, and ORF3 of avian HEV and reference HEV isolates. Phylogenetic tree constructed using the maximum likelihood (ML) method in PhyML v3.0, under the GTR+Γ+I model. The analysis includes 1000 replicates of the alignment, with bootstrap values indicated at nodes (>70% shown). The red dot denotes the sequence determined in this study. (B) Recombination within the genome of avian HEV strain GDZQ122. Bootscan analysis of the complete genome sequence of avian HEV strain GDZQ122 was conducted using SimPlot program. Parameters: 200 bp window size, 20 bp step size, GapStrip: On, 100 replicates, Kimura (2-parameter), and a T/t ratio of 2.0 in Neighbor-Joining analysis. The phylogenetic trees reconstructed based on three regions of the genome (1–1846, 1847–3014, and 3015–6610) using the maximum likelihood (ML) method in PhyML v3.0 under the best-fit substitution model.

    Journal: Poultry Science

    Article Title: Research note: Genetically diverse avian hepatitis E virus identified in chickens with hepatitis-splenomegaly syndrome in Guangdong Province, China

    doi: 10.1016/j.psj.2024.104557

    Figure Lengend Snippet: Genetic characterization of avian HEV. (A) Phylogenetic analysis based on the complete nucleotide sequences of ORF1, ORF2, and ORF3 of avian HEV and reference HEV isolates. Phylogenetic tree constructed using the maximum likelihood (ML) method in PhyML v3.0, under the GTR+Γ+I model. The analysis includes 1000 replicates of the alignment, with bootstrap values indicated at nodes (>70% shown). The red dot denotes the sequence determined in this study. (B) Recombination within the genome of avian HEV strain GDZQ122. Bootscan analysis of the complete genome sequence of avian HEV strain GDZQ122 was conducted using SimPlot program. Parameters: 200 bp window size, 20 bp step size, GapStrip: On, 100 replicates, Kimura (2-parameter), and a T/t ratio of 2.0 in Neighbor-Joining analysis. The phylogenetic trees reconstructed based on three regions of the genome (1–1846, 1847–3014, and 3015–6610) using the maximum likelihood (ML) method in PhyML v3.0 under the best-fit substitution model.

    Article Snippet: Simplot analysis using the bootscan method confirmed this recombination event and indicated two recombination breakpoints at nucleotide positions 1,847 and 3,014 ( B).

    Techniques: Construct, Sequencing