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bootscan analysis simplot software v3.5  (Simplot Science)

 
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    Simplot Science bootscan analysis simplot software v3.5
    Bootscan Analysis Simplot Software V3.5, 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
    https://www.bioz.com/result/bootscan analysis simplot software v3.5/product/Simplot Science
    Average 90 stars, based on 1 article reviews
    bootscan analysis simplot software v3.5 - by Bioz Stars, 2026-04
    90/100 stars

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    Similarity plots and Bootscan analyses of potential HCV recombinants determined on the basis of the IRES complete sequence using Simplot version 3.5.1 and Simplot ++ V1.3 software. Simplot++ analyses (left panels) display the percentage of sequence similarity over the IRES sequences of the HCV genome (nucleotide positions 41 to 359 according to strain 1a H77 numbering). Bootscan analysis (right panels) shows the percentage of permuted trees (y-axis). This approach permits to observe levels of phylogenetic relatedness between a query sequence and a reference sequence in different genomic regions. Query sequences (shown on the upper part of the figure) correspond to ( A ) clone B12 (putative 1a/3a recombinant), ( B ) clone C4 (putative 3a/1a recombinant), and ( C ) clone A33 (putative 3a/1a recombinant). Reference and/or putative parental sequences are indicated in purple for genotype 1a (strain H77, NCBI Accession No. AF009606) and green for genotype 3a (strain NZL1, NCBI Accession No. D17763). All analyses were performed using a 100 bp sliding window and a 10 bp step size. For Simplot++ analyses, a GTR optimized model of nucleotide substitution was employed, whereas for Bootscan, a Kimura two-parameter model was used.

    Journal: Viruses

    Article Title: Mixed Infections Unravel Novel HCV Inter-Genotypic Recombinant Forms within the Conserved IRES Region

    doi: 10.3390/v16040560

    Figure Lengend Snippet: Similarity plots and Bootscan analyses of potential HCV recombinants determined on the basis of the IRES complete sequence using Simplot version 3.5.1 and Simplot ++ V1.3 software. Simplot++ analyses (left panels) display the percentage of sequence similarity over the IRES sequences of the HCV genome (nucleotide positions 41 to 359 according to strain 1a H77 numbering). Bootscan analysis (right panels) shows the percentage of permuted trees (y-axis). This approach permits to observe levels of phylogenetic relatedness between a query sequence and a reference sequence in different genomic regions. Query sequences (shown on the upper part of the figure) correspond to ( A ) clone B12 (putative 1a/3a recombinant), ( B ) clone C4 (putative 3a/1a recombinant), and ( C ) clone A33 (putative 3a/1a recombinant). Reference and/or putative parental sequences are indicated in purple for genotype 1a (strain H77, NCBI Accession No. AF009606) and green for genotype 3a (strain NZL1, NCBI Accession No. D17763). All analyses were performed using a 100 bp sliding window and a 10 bp step size. For Simplot++ analyses, a GTR optimized model of nucleotide substitution was employed, whereas for Bootscan, a Kimura two-parameter model was used.

    Article Snippet: Moreover, the Bootscan graphs generated by Simplot software (version 3.5.1) indicated similar results ( , right panels).

    Techniques: Sequencing, Software, Recombinant

    Recombination events detected by RDP4 in HCV IRES clones from sample 05.

    Journal: Viruses

    Article Title: Mixed Infections Unravel Novel HCV Inter-Genotypic Recombinant Forms within the Conserved IRES Region

    doi: 10.3390/v16040560

    Figure Lengend Snippet: Recombination events detected by RDP4 in HCV IRES clones from sample 05.

    Article Snippet: Moreover, the Bootscan graphs generated by Simplot software (version 3.5.1) indicated similar results ( , right panels).

    Techniques: Clone Assay, Recombinant, Sequencing