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bootscanning and informative site performed by simplot 3.5.1 software  (Simplot Science)

 
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    Simplot Science bootscanning and informative site performed by simplot 3.5.1 software
    Bootscanning And Informative Site Performed By Simplot 3.5.1 Software, 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/bootscanning+analysis+simplot+3+5+1/pm32115719-25-16-15
    Average 90 stars, based on 1 article reviews
    bootscanning and informative site performed by simplot 3.5.1 software - by Bioz Stars, 2026-09
    90/100 stars

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    Related Articles

    other:

    Article Title: Multiple CRF01_AE/CRF07_BC Recombinants Enhanced the HIV-1 Epidemic Complexity Among MSM in Shenyang City, Northeast China
    Article Snippet: Recombination fragments (as determined using jpHMM and Simplot bootscanning) were phylogenetically studied using IQ-Tree v2.0.5.

    Article Title: Genetic Dynamic Analysis of the Influenza A H5N1 NS1 Gene in China
    Article Snippet: For each sample, the eight gene segment alignments were manually concatenated in the order of their length to generate a single alignment of full genome sequences, and the resulting alignment was analyzed using the bootscanning method implemented in the SimPlot v3.5.1 .

    Article Title: Identification of a novel CRF01_AE/CRF07_BC (CRF163_0107) circulating recombinant form in Shenyang city, the economic center of Northeast China.
    Article Snippet: Bootscanning in Simplot (version 3.5.1) and RIP online tools(RIP 3.0 submission form (lanl.gov)) analyses were used to identify the recombination patterns.

    Article Title: Phylodynamics of HIV-1 Circulating Recombinant Forms 12_BF and 38_BF in Argentina and Uruguay
    Article Snippet: Two strategies were used to characterize the HIV-1 pol sequences used in the present study as CRF12_BF-like or CRF38_BF-like recombinants: 1) First, the recombination breakpoints of each sequence were identified by Bootscanning using Simplot version 3.5.1 [ ].

    Article Title: Phylodynamics of HIV-1 Subtype C Epidemic in East Africa
    Article Snippet: Putative intrasubtype C/C′ recombinant sequences in Ethiopia were identified by Bootscanning using Simplot version 3.5.1 , following the same procedure described by Pollakis et al . Bootstrap values supporting branching with reference sequences were determined in Neighbor-Joining (NJ) trees constructed using the K2-P nucleotide substitution model, based on 100 re-samplings, with a 300 bp sliding window moving in steps of 10 bases.

    Software:

    Article Title: HIV-1 genetic diversity and transmitted drug resistance among newly diagnosed HIV-1 individuals in Jiangmen, China.
    Article Snippet: Correspondence Guifang Hu, School of Public Health, Southern Medical University, No.1023, South Shatai Road, Baiyun District, Guangzhou, Guangdong 510515, China Telephone number: +86-18933940199 E-mail: guif_hu@sina.com Funding information Guangdong Province Public Welfare Research and Capacity Building Project, Grant number: 2014B020212007; Guangzhou Science and Technology Project, Grant number: 201508020018



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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