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bootscan analysis simplot version 3.5.1  (Simplot Science)

 
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    Simplot Science bootscan analysis simplot version 3.5.1
    Bootscan Analysis Simplot 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
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    Average 90 stars, based on 1 article reviews
    bootscan analysis simplot version 3.5.1 - by Bioz Stars, 2026-03
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    bootscanning analysis simplot version 3.5.1  (Simplot Science)
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    Bootscanning analysis of <t>recombination</t> for complete ORF sequences using a 600 bp window, a 20 bp step increment and 1000 bootstrap replicates. Genotypes 1 and 2 are shown as the red and green lines, respectively, while the grey line represents the outlier genotype 4. The dashed line indicates the 80 % threshold used to denote significance between genotypes. (a) Cin03 is a non-recombinant genotype 2 isolate. (b) Cin08 is a non-recombinant genotype 2 isolate. (c) Cin11 is a genotype 2 → 1 → 2 recombinant isolate. (d) VCU02 is a genotype 1 → 2 → 1 → 2 → 1 recombinant isolate.
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    Bootscan analysis of recombinant CAstV sequences for confirming recombination was performed using Simplot program v3.5.1. Each analysis considers different parent sequences (different colors) plotted in a graph considering in the vertical-axis Percentage of permuted trees, and on the horizontal axis, position on the genome of the query sequence. Recombinant CAstV query sequences are 19-0981/CA-SK/19 ; Biii-ANAND/IN/2016 ; Bi-GDYHTJ718-6/CN/2018 ; 18-0942/CA-SK/18 ; 19-0935/CA-SK/19 ; CC_CkAstV/US/2014 ; and Bii-GA2011/US/2011 .

    Journal: Viruses

    Article Title: Chicken Astrovirus (CAstV) Molecular Studies Reveal Evidence of Multiple Past Recombination Events in Sequences Originated from Clinical Samples of White Chick Syndrome (WCS) in Western Canada

    doi: 10.3390/v12101096

    Figure Lengend Snippet: Bootscan analysis of recombinant CAstV sequences for confirming recombination was performed using Simplot program v3.5.1. Each analysis considers different parent sequences (different colors) plotted in a graph considering in the vertical-axis Percentage of permuted trees, and on the horizontal axis, position on the genome of the query sequence. Recombinant CAstV query sequences are 19-0981/CA-SK/19 ; Biii-ANAND/IN/2016 ; Bi-GDYHTJ718-6/CN/2018 ; 18-0942/CA-SK/18 ; 19-0935/CA-SK/19 ; CC_CkAstV/US/2014 ; and Bii-GA2011/US/2011 .

    Article Snippet: Putative recombination sequences were further investigated by using Bootscan analysis within the Simplot program version 3.5.1 [ ], using the following parameters: window size = 400 bp; step size = 40 bp; GapStrip = On; Repetitions = 100; Kimura 2-parameter substitution model; T/t = 2; and using the neighbor-joining method [ , , ].

    Techniques: Recombinant, Sequencing

    CAstV recombinant sequences and parents/parent-like sequences detected by 6 recombination methods in RDP5, ML phylogenetic trees, and Bootscan analysis in SimPlot software.

    Journal: Viruses

    Article Title: Chicken Astrovirus (CAstV) Molecular Studies Reveal Evidence of Multiple Past Recombination Events in Sequences Originated from Clinical Samples of White Chick Syndrome (WCS) in Western Canada

    doi: 10.3390/v12101096

    Figure Lengend Snippet: CAstV recombinant sequences and parents/parent-like sequences detected by 6 recombination methods in RDP5, ML phylogenetic trees, and Bootscan analysis in SimPlot software.

    Article Snippet: Putative recombination sequences were further investigated by using Bootscan analysis within the Simplot program version 3.5.1 [ ], using the following parameters: window size = 400 bp; step size = 40 bp; GapStrip = On; Repetitions = 100; Kimura 2-parameter substitution model; T/t = 2; and using the neighbor-joining method [ , , ].

    Techniques: Recombinant, Software, Sequencing

    The number of algorithms of the RDP4 package that were predicting the recombination event and recombinant score are shown.

    Journal: Scientific Reports

    Article Title: Genome Analysis of A Novel Recombinant Human Adenovirus Type 1 in China

    doi: 10.1038/s41598-018-37756-4

    Figure Lengend Snippet: The number of algorithms of the RDP4 package that were predicting the recombination event and recombinant score are shown.

    Article Snippet: Bootscan analysis in the SimPlot package version 3.5.1 was used to test potential recombination events.

    Techniques: Recombinant

    Bootscanning analysis of recombination for complete ORF sequences using a 600 bp window, a 20 bp step increment and 1000 bootstrap replicates. Genotypes 1 and 2 are shown as the red and green lines, respectively, while the grey line represents the outlier genotype 4. The dashed line indicates the 80 % threshold used to denote significance between genotypes. (a) Cin03 is a non-recombinant genotype 2 isolate. (b) Cin08 is a non-recombinant genotype 2 isolate. (c) Cin11 is a genotype 2 → 1 → 2 recombinant isolate. (d) VCU02 is a genotype 1 → 2 → 1 → 2 → 1 recombinant isolate.

    Journal: The Journal of General Virology

    Article Title: Recombination among GB virus C (GBV-C) isolates in the United States

    doi: 10.1099/jgv.0.000477

    Figure Lengend Snippet: Bootscanning analysis of recombination for complete ORF sequences using a 600 bp window, a 20 bp step increment and 1000 bootstrap replicates. Genotypes 1 and 2 are shown as the red and green lines, respectively, while the grey line represents the outlier genotype 4. The dashed line indicates the 80 % threshold used to denote significance between genotypes. (a) Cin03 is a non-recombinant genotype 2 isolate. (b) Cin08 is a non-recombinant genotype 2 isolate. (c) Cin11 is a genotype 2 → 1 → 2 recombinant isolate. (d) VCU02 is a genotype 1 → 2 → 1 → 2 → 1 recombinant isolate.

    Article Snippet: To identify possible recombination events, bootscanning analysis of complete ORF sequences was performed as implemented in SimPlot version 3.5.1 using the Kimura 2-parameter with a 600 base pair (bp) window, a 20 bp step increment and 1000 bootstrap replicates ( Lole et al. , 1999 ).

    Techniques: Recombinant