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bootscan graphs generated by simplot software version 3.5.1  (Simplot Science)

 
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    Simplot Science bootscan graphs generated by simplot software version 3.5.1
    Bootscan Graphs Generated By Simplot Software Version 3.5.1, 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/product/bootscan+software/bootscan+analysis+simplot+version+3+5+1/pm38675902-146-2-6
    Average 90 stars, based on 1 article reviews
    bootscan graphs generated by simplot software version 3.5.1 - by Bioz Stars, 2026-09
    90/100 stars

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    Related Articles

    Isolation:

    Article Title: Uncovering the Prevalence and Genetic Characterization of Rabbit-Derived Paslahepevirus Balayani (Hepatitis E Virus) in Hebei Province, China.
    Article Snippet: Paslahepevirus balayani (hepatitis E virus) is a zoonotic pathogen, with rabbit Paslahepevirus balayani (HEV-3ra) being widely distributed among global rabbit populations.. Notably, in China, rabbits constitute a significant HEV host, second only to swine.. Emerging evidence suggests that HEV-3ra possesses the capability to cross species barriers and infect humans.

    Immunofluorescence:

    Article Title: Discovery of a novel Betacoronavirus 1, cpCoV, in goats in China: The new risk of cross-species transmission.
    Article Snippet: .. Bootscan analysis was performed with Simplot, version 3.5.1. https://doi.org/10.1371/journal.ppat.1012974.g003 PLOS Pathogens | https://doi.org/10.1371/journal.ppat.1012974 March 18, 2025 14 / 23 three blind passages, the challenge group samples induced a CPE, and the cell cultures were identified as cpCoV-positive by RT-qPCR, RT-PCR, and IFA methods. ..

    Software:

    Article Title: Identification of a novel HIV-1 third-generation circulating recombinant form (CRF126_0755) in Guangdong, China.
    Article Snippet: .. Branches with bootstrap values greater than 70% were considered reliable, and the values are shown at the nodes. (B) BootScan analysis, performed using SimPlot 3.5 software with a window size of 300 bp and step size of 20 bp. (C) Genome mosaic map of CRF126_0755 NFLG, generated using the LANL Recombinant HIV-1 Drawing Tool (https:// www. hiv. lanl. gov/ conte nt/ seque nce/ DRAW_ CRF/ recom_ mapper. html) in almost all CRF55_01B strains, was found in all four CRF126-0755 NFLGs, possibly conferring increased drug resistance [17]. ..

    Generated:

    Article Title: Identification of a novel HIV-1 third-generation circulating recombinant form (CRF126_0755) in Guangdong, China.
    Article Snippet: .. Branches with bootstrap values greater than 70% were considered reliable, and the values are shown at the nodes. (B) BootScan analysis, performed using SimPlot 3.5 software with a window size of 300 bp and step size of 20 bp. (C) Genome mosaic map of CRF126_0755 NFLG, generated using the LANL Recombinant HIV-1 Drawing Tool (https:// www. hiv. lanl. gov/ conte nt/ seque nce/ DRAW_ CRF/ recom_ mapper. html) in almost all CRF55_01B strains, was found in all four CRF126-0755 NFLGs, possibly conferring increased drug resistance [17]. ..

    Article Title: Mixed Infections Unravel Novel HCV Inter-Genotypic Recombinant Forms within the Conserved IRES Region.
    Article Snippet: .. Moreover, the Bootscan graphs generated by Simplot software (version 3.5.1) indicated similar results (Figure 3, right panels). ..

    Recombinant:

    Article Title: Identification of a novel HIV-1 third-generation circulating recombinant form (CRF126_0755) in Guangdong, China.
    Article Snippet: .. Branches with bootstrap values greater than 70% were considered reliable, and the values are shown at the nodes. (B) BootScan analysis, performed using SimPlot 3.5 software with a window size of 300 bp and step size of 20 bp. (C) Genome mosaic map of CRF126_0755 NFLG, generated using the LANL Recombinant HIV-1 Drawing Tool (https:// www. hiv. lanl. gov/ conte nt/ seque nce/ DRAW_ CRF/ recom_ mapper. html) in almost all CRF55_01B strains, was found in all four CRF126-0755 NFLGs, possibly conferring increased drug resistance [17]. ..

    other:

    Article Title: Whole-Genome Analysis of Porcine Epidemic Diarrhea Virus from Yunnan, China.
    Article Snippet: The above methods were further validated and confirmed for the presence of genome recombination and break sites using BootScan in Simplot software, with the BootScan window size set to 400 bp, the gap size set to 40 bp, and other parameters set to default values.

    Article Title: Genetic characterization of a novel HIV-1 circulating recombinant form (CRF162_cpx) involving CRF01_AE, CRF07_BC and subtype B in Guangdong, China.
    Article Snippet: Human immunodeficiency virus type 1 (HIV-1) is characterized by its extremely high level of genetic diversity.. The spread of different subtypes in the same population often leads to the emergence of circulating recombinant forms (CRFs) and unique recombinant forms (URFs).. At present, the main recombinant subtypes of HIV-1 in China originate from CRF07_BC, CRF01_AE, CRF55_01B and subtype B.

    Article Title: Identification of a novel HIV-1 third-generation circulating recombinant form (CRF126_0755) in Guangdong, China.
    Article Snippet: The sequences were analyzed using jpHMM (http:// jpHMM. gobics. de/ submi ssion_ hiv. html), RIP (https:// www. hiv. lanl. gov/ conte nt/ seque nce/ RIP/ RIP. html), and BootScan (Simplot software V3.5.1) with a window size of 350 bp and steps of 20 bp.



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    Image Search Results


    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