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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/product/bootscan+in+simplot+software/bootscan+analysis+simplot+version+3+5+1/pm39681761-64-0-6
    Average 90 stars, based on 1 article reviews
    bootscan analysis simplot software v3.5 - by Bioz Stars, 2026-10
    90/100 stars

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    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.



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    <t>The</t> <t>phylogenetic</t> inferences were performed by the Neighbor-Joining algorithm under the Kimura-2 parameter nucleotide substitution model using the MEGA v5.0 package. The scale represents the number of substitutions per site. Cape Verde and reference sequences are represented, respectively as black and white circles. Bootscan analyses of HIV-1 major URF samples are displayed. Recombinant profiles were inferred using a sliding window of 200 bp, steps of 20 bp and the Kimura-2 parameters model using SimPlot <t>3.5.1</t> software. Reference samples corresponding to the major HIV-1 subtypes are indicated by different colors.
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    The phylogenetic inferences were performed by the Neighbor-Joining algorithm under the Kimura-2 parameter nucleotide substitution model using the MEGA v5.0 package. The scale represents the number of substitutions per site. Cape Verde and reference sequences are represented, respectively as black and white circles. Bootscan analyses of HIV-1 major URF samples are displayed. Recombinant profiles were inferred using a sliding window of 200 bp, steps of 20 bp and the Kimura-2 parameters model using SimPlot 3.5.1 software. Reference samples corresponding to the major HIV-1 subtypes are indicated by different colors.

    Journal: PLoS ONE

    Article Title: Profile of the HIV Epidemic in Cape Verde: Molecular Epidemiology and Drug Resistance Mutations among HIV-1 and HIV-2 Infected Patients from Distinct Islands of the Archipelago

    doi: 10.1371/journal.pone.0096201

    Figure Lengend Snippet: The phylogenetic inferences were performed by the Neighbor-Joining algorithm under the Kimura-2 parameter nucleotide substitution model using the MEGA v5.0 package. The scale represents the number of substitutions per site. Cape Verde and reference sequences are represented, respectively as black and white circles. Bootscan analyses of HIV-1 major URF samples are displayed. Recombinant profiles were inferred using a sliding window of 200 bp, steps of 20 bp and the Kimura-2 parameters model using SimPlot 3.5.1 software. Reference samples corresponding to the major HIV-1 subtypes are indicated by different colors.

    Article Snippet: Subtype determination was performed by: 1) the REGA program , ; 2) Neighbor-Joining (NJ) phylogenetic analyses using MEGA program , and 3) Bootscan analyses with Simplot 3.5.1 software .

    Techniques: Recombinant, Software

    (A) The phylogenetic inferences were performed by the Neighbor-Joining algorithm under the Kimura-2 parameter nucleotide substitution model using the MEGA v5.0 package. The scale represents the number of substitutions per site. Cape Verde and reference sequences are represented respectively as colored and white circles. (B) Recombinant profiles were inferred using a sliding window of 200 bp, steps of 20 bp and the Kimura-2 parameters model using SimPlot 3.5.1 software. Reference samples corresponding to the major HIV-1 subtypes are indicated by different colors. Partial NJ phylogenetic trees using K-2p model were performed for bootscan fragments under 70% and were represented as I - 150 bp and II and III - 300 bp.

    Journal: PLoS ONE

    Article Title: Profile of the HIV Epidemic in Cape Verde: Molecular Epidemiology and Drug Resistance Mutations among HIV-1 and HIV-2 Infected Patients from Distinct Islands of the Archipelago

    doi: 10.1371/journal.pone.0096201

    Figure Lengend Snippet: (A) The phylogenetic inferences were performed by the Neighbor-Joining algorithm under the Kimura-2 parameter nucleotide substitution model using the MEGA v5.0 package. The scale represents the number of substitutions per site. Cape Verde and reference sequences are represented respectively as colored and white circles. (B) Recombinant profiles were inferred using a sliding window of 200 bp, steps of 20 bp and the Kimura-2 parameters model using SimPlot 3.5.1 software. Reference samples corresponding to the major HIV-1 subtypes are indicated by different colors. Partial NJ phylogenetic trees using K-2p model were performed for bootscan fragments under 70% and were represented as I - 150 bp and II and III - 300 bp.

    Article Snippet: Subtype determination was performed by: 1) the REGA program , ; 2) Neighbor-Joining (NJ) phylogenetic analyses using MEGA program , and 3) Bootscan analyses with Simplot 3.5.1 software .

    Techniques: Recombinant, Software