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similarity plots and bootscan analyses simplot software package v3.5.1  (Simplot Science)

 
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    Simplot Science similarity plots and bootscan analyses simplot software package v3.5.1
    Similarity Plots And Bootscan Analyses Simplot Software Package V3.5.1, 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+in+simplot+software/similarity+plot+and+bootscan+analyses+in+simplot+software/pm39342978-76-17-24
    Average 90 stars, based on 1 article reviews
    similarity plots and bootscan analyses simplot software package v3.5.1 - by Bioz Stars, 2026-10
    90/100 stars

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    Related Articles

    Recombinant:

    Article Title: Detection and sequence analysis of Canine morbillivirus in multiple species of the Mustelidae family.
    Article Snippet: .. The potential recombinant CDV genomes were tested through recombination analysis using similarity plot and bootscan analyses in SimPlot software package (version 3.5.1.) ..

    Article Title: The emergence of an unassigned complex recombinant form in a Pakistani HIV-infected individual.
    Article Snippet: In Pakistan, the HIV situation has gone from an outbreak to a concentrated epidemic, and the virus has now crossed into the low-risk population.. In addition, several new HIV outbreaks have occurred in different parts of the country.. HIV-1 subtype A has been the major epidemic subtype in Pakistan; however, as the epidemic has grown, the emergence of several new subtypes and recombinant forms has been observed.

    Article Title: Genetic and evolutionary analysis of a new Asia-4 lineage and naturally recombinant canine distemper virus strains from Thailand
    Article Snippet: .. The potential recombinant CDV genomes were then subjected to further recombination analysis using similarity plot and bootscan analyses in SimPlot software package version 3.5.1 . ..

    Article Title: Phylogenetic evidence of a novel lineage of canine pneumovirus and a naturally recombinant strain isolated from dogs with respiratory illness in Thailand
    Article Snippet: .. The potential recombinant CPV genomes were further subjected to recombination analysis using a similarity plot and bootscan analyses in the SimPlot software package version 3.5.1 [ ]. ..

    Generated:

    Article Title: The emergence of an unassigned complex recombinant form in a Pakistani HIV-infected individual.
    Article Snippet: In Pakistan, the HIV situation has gone from an outbreak to a concentrated epidemic, and the virus has now crossed into the low-risk population.. In addition, several new HIV outbreaks have occurred in different parts of the country.. HIV-1 subtype A has been the major epidemic subtype in Pakistan; however, as the epidemic has grown, the emergence of several new subtypes and recombinant forms has been observed.

    Sequencing:

    Article Title: The emergence of an unassigned complex recombinant form in a Pakistani HIV-infected individual.
    Article Snippet: In Pakistan, the HIV situation has gone from an outbreak to a concentrated epidemic, and the virus has now crossed into the low-risk population.. In addition, several new HIV outbreaks have occurred in different parts of the country.. HIV-1 subtype A has been the major epidemic subtype in Pakistan; however, as the epidemic has grown, the emergence of several new subtypes and recombinant forms has been observed.

    Article Title: Diversity and genetic characterization of orthohantavirus from small mammals and humans during 2012-2022 in Hubei Province, Central China.
    Article Snippet: .. In addition, similarity plots and bootscan analysis methods in Simplot version 3.5.1 were used to analyze the sequence alignment (Samson et al., 2022). ..

    other:

    Article Title: Chevrier’s Field Mouse ( Apodemus chevrieri ) and Père David’s Vole ( Eothenomys melanogaster ) in China Carry Orthohepeviruses that form Two Putative Novel Genotypes Within the Species Orthohepevirus C
    Article Snippet: The aa identity plot from bootscan analyses with Simplot V3.5 (Lole et al. 1999 ) demonstrated that the novel rodent orthohepevirus strains had no evidence of recombination between ORF1- and ORF2-encoded aa sequences compared to reference strains of Orthohepevirus A to Orthohepevirus D (Supplementary Figure S1).

    Article Title: Contribution of transgender sex workers to the complexity of the HIV-1 epidemic in the metropolitan area of Milan.
    Article Snippet: For sequences with unassigned subtype, similarity and bootscanning plots implemented in the SimPlot v.3.5.2 (http:// sray. med. som. jhmi. edu/ SCRoftware/ simplot/) were used to reconstruct recombination pattern.



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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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    Image Search Results


    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