bootscan analyses implemented in Search Results


simplot v.3.5.1 program  (Simplot Science)
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Simplot Science simplot v.3.5.1 program
Simplot V.3.5.1 Program, 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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bootscan analysis (as implemented in simplot)  (Simplot Science)
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Simplot Science bootscan analysis (as implemented in simplot)
Bootscan Analysis (As Implemented In Simplot), 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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bootscan implemented in simplot v3.5.1 software  (Simplot Science)
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Simplot Science bootscan implemented in simplot v3.5.1 software
Bootscan Implemented In Simplot V3.5.1 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
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bootscan  (Simplot Science)
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Simplot Science bootscan
Nucleotide sequence recombination analysis of the whole genome and the hexon gene of HAdV-E4FSl. The genome of HAdV-E4FSl (AY599837) was analyzed for sequence recombination events with HAdV and SAdV genomes using the software Simplot, which is available on-line (http://sray.med.som.jhmi.edu/SCRoftware/simplot/). <t>Bootscan</t> analysis of the genome (A) and hexon (B) shows a lateral transfer of a portion of the hexon gene from HAdV-B 16. These are supported by the Simplot analysis of the genome (C) and hexon (D). Unlike the Simplot panels (C and D), only the SAdV-E26 genome, rather than the entire set of SAdV-E22 through -E26 sequences, is presented in the Bootscan panels (A and B), as similar genomes compete out the signal. For Bootscan, removing four of the five genomes and repeating the analysis with each individually, gives a clearer representation, reflecting the Simplot result for the highest similarity match. MAFFT software was used to align the sequences prior to recombination analysis (http://mafft.cbrc.jp/alignment/server/). Default parameter settings for the Simplot software were used for analyzing the hexon sequences: window size (200 nucleotides [nt]), step size (20 nt), replicates used (n=100), gap stripping (on), distance model (Kimura) and tree model (neighbor-joining). Similarly, whole genomes were analyzed, beginning with an initial alignment using MAFFT and following with recombination analysis using Simplot and Bootscan. Only the window size and step size were altered for the genome analysis (1000 and 200, respectively), with the rest of the default parameters unchanged. Genome nucleotide positions are noted along the x-axis, and the percentages of permutated trees that supported grouping are marked along the y-axis. For reference, select genome and gene-specific landmarks are noted above each graph. Colors: pink, SAdV-E26 and green, HAdV-B16.
Bootscan, 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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bootscanning simplot version 3.5.1  (Simplot Science)
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Simplot Science bootscanning simplot version 3.5.1
Nucleotide sequence recombination analysis of the whole genome and the hexon gene of HAdV-E4FSl. The genome of HAdV-E4FSl (AY599837) was analyzed for sequence recombination events with HAdV and SAdV genomes using the software Simplot, which is available on-line (http://sray.med.som.jhmi.edu/SCRoftware/simplot/). <t>Bootscan</t> analysis of the genome (A) and hexon (B) shows a lateral transfer of a portion of the hexon gene from HAdV-B 16. These are supported by the Simplot analysis of the genome (C) and hexon (D). Unlike the Simplot panels (C and D), only the SAdV-E26 genome, rather than the entire set of SAdV-E22 through -E26 sequences, is presented in the Bootscan panels (A and B), as similar genomes compete out the signal. For Bootscan, removing four of the five genomes and repeating the analysis with each individually, gives a clearer representation, reflecting the Simplot result for the highest similarity match. MAFFT software was used to align the sequences prior to recombination analysis (http://mafft.cbrc.jp/alignment/server/). Default parameter settings for the Simplot software were used for analyzing the hexon sequences: window size (200 nucleotides [nt]), step size (20 nt), replicates used (n=100), gap stripping (on), distance model (Kimura) and tree model (neighbor-joining). Similarly, whole genomes were analyzed, beginning with an initial alignment using MAFFT and following with recombination analysis using Simplot and Bootscan. Only the window size and step size were altered for the genome analysis (1000 and 200, respectively), with the rest of the default parameters unchanged. Genome nucleotide positions are noted along the x-axis, and the percentages of permutated trees that supported grouping are marked along the y-axis. For reference, select genome and gene-specific landmarks are noted above each graph. Colors: pink, SAdV-E26 and green, HAdV-B16.
Bootscanning 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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similarity plot and bootscanning analysis  (Simplot Science)
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Simplot Science similarity plot and bootscanning analysis
Nucleotide sequence recombination analysis of the whole genome and the hexon gene of HAdV-E4FSl. The genome of HAdV-E4FSl (AY599837) was analyzed for sequence recombination events with HAdV and SAdV genomes using the software Simplot, which is available on-line (http://sray.med.som.jhmi.edu/SCRoftware/simplot/). <t>Bootscan</t> analysis of the genome (A) and hexon (B) shows a lateral transfer of a portion of the hexon gene from HAdV-B 16. These are supported by the Simplot analysis of the genome (C) and hexon (D). Unlike the Simplot panels (C and D), only the SAdV-E26 genome, rather than the entire set of SAdV-E22 through -E26 sequences, is presented in the Bootscan panels (A and B), as similar genomes compete out the signal. For Bootscan, removing four of the five genomes and repeating the analysis with each individually, gives a clearer representation, reflecting the Simplot result for the highest similarity match. MAFFT software was used to align the sequences prior to recombination analysis (http://mafft.cbrc.jp/alignment/server/). Default parameter settings for the Simplot software were used for analyzing the hexon sequences: window size (200 nucleotides [nt]), step size (20 nt), replicates used (n=100), gap stripping (on), distance model (Kimura) and tree model (neighbor-joining). Similarly, whole genomes were analyzed, beginning with an initial alignment using MAFFT and following with recombination analysis using Simplot and Bootscan. Only the window size and step size were altered for the genome analysis (1000 and 200, respectively), with the rest of the default parameters unchanged. Genome nucleotide positions are noted along the x-axis, and the percentages of permutated trees that supported grouping are marked along the y-axis. For reference, select genome and gene-specific landmarks are noted above each graph. Colors: pink, SAdV-E26 and green, HAdV-B16.
Similarity Plot And Bootscanning Analysis, 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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bootscanning method  (Simplot Science)
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Simplot Science bootscanning method
Nucleotide sequence recombination analysis of the whole genome and the hexon gene of HAdV-E4FSl. The genome of HAdV-E4FSl (AY599837) was analyzed for sequence recombination events with HAdV and SAdV genomes using the software Simplot, which is available on-line (http://sray.med.som.jhmi.edu/SCRoftware/simplot/). <t>Bootscan</t> analysis of the genome (A) and hexon (B) shows a lateral transfer of a portion of the hexon gene from HAdV-B 16. These are supported by the Simplot analysis of the genome (C) and hexon (D). Unlike the Simplot panels (C and D), only the SAdV-E26 genome, rather than the entire set of SAdV-E22 through -E26 sequences, is presented in the Bootscan panels (A and B), as similar genomes compete out the signal. For Bootscan, removing four of the five genomes and repeating the analysis with each individually, gives a clearer representation, reflecting the Simplot result for the highest similarity match. MAFFT software was used to align the sequences prior to recombination analysis (http://mafft.cbrc.jp/alignment/server/). Default parameter settings for the Simplot software were used for analyzing the hexon sequences: window size (200 nucleotides [nt]), step size (20 nt), replicates used (n=100), gap stripping (on), distance model (Kimura) and tree model (neighbor-joining). Similarly, whole genomes were analyzed, beginning with an initial alignment using MAFFT and following with recombination analysis using Simplot and Bootscan. Only the window size and step size were altered for the genome analysis (1000 and 200, respectively), with the rest of the default parameters unchanged. Genome nucleotide positions are noted along the x-axis, and the percentages of permutated trees that supported grouping are marked along the y-axis. For reference, select genome and gene-specific landmarks are noted above each graph. Colors: pink, SAdV-E26 and green, HAdV-B16.
Bootscanning Method, 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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software version 3.5.1  (Simplot Science)
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Simplot Science software version 3.5.1
Nucleotide sequence recombination analysis of the whole genome and the hexon gene of HAdV-E4FSl. The genome of HAdV-E4FSl (AY599837) was analyzed for sequence recombination events with HAdV and SAdV genomes using the software Simplot, which is available on-line (http://sray.med.som.jhmi.edu/SCRoftware/simplot/). <t>Bootscan</t> analysis of the genome (A) and hexon (B) shows a lateral transfer of a portion of the hexon gene from HAdV-B 16. These are supported by the Simplot analysis of the genome (C) and hexon (D). Unlike the Simplot panels (C and D), only the SAdV-E26 genome, rather than the entire set of SAdV-E22 through -E26 sequences, is presented in the Bootscan panels (A and B), as similar genomes compete out the signal. For Bootscan, removing four of the five genomes and repeating the analysis with each individually, gives a clearer representation, reflecting the Simplot result for the highest similarity match. MAFFT software was used to align the sequences prior to recombination analysis (http://mafft.cbrc.jp/alignment/server/). Default parameter settings for the Simplot software were used for analyzing the hexon sequences: window size (200 nucleotides [nt]), step size (20 nt), replicates used (n=100), gap stripping (on), distance model (Kimura) and tree model (neighbor-joining). Similarly, whole genomes were analyzed, beginning with an initial alignment using MAFFT and following with recombination analysis using Simplot and Bootscan. Only the window size and step size were altered for the genome analysis (1000 and 200, respectively), with the rest of the default parameters unchanged. Genome nucleotide positions are noted along the x-axis, and the percentages of permutated trees that supported grouping are marked along the y-axis. For reference, select genome and gene-specific landmarks are noted above each graph. Colors: pink, SAdV-E26 and green, HAdV-B16.
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
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bootscanning  (Simplot Science)
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Simplot Science bootscanning
Nucleotide sequence recombination analysis of the whole genome and the hexon gene of HAdV-E4FSl. The genome of HAdV-E4FSl (AY599837) was analyzed for sequence recombination events with HAdV and SAdV genomes using the software Simplot, which is available on-line (http://sray.med.som.jhmi.edu/SCRoftware/simplot/). <t>Bootscan</t> analysis of the genome (A) and hexon (B) shows a lateral transfer of a portion of the hexon gene from HAdV-B 16. These are supported by the Simplot analysis of the genome (C) and hexon (D). Unlike the Simplot panels (C and D), only the SAdV-E26 genome, rather than the entire set of SAdV-E22 through -E26 sequences, is presented in the Bootscan panels (A and B), as similar genomes compete out the signal. For Bootscan, removing four of the five genomes and repeating the analysis with each individually, gives a clearer representation, reflecting the Simplot result for the highest similarity match. MAFFT software was used to align the sequences prior to recombination analysis (http://mafft.cbrc.jp/alignment/server/). Default parameter settings for the Simplot software were used for analyzing the hexon sequences: window size (200 nucleotides [nt]), step size (20 nt), replicates used (n=100), gap stripping (on), distance model (Kimura) and tree model (neighbor-joining). Similarly, whole genomes were analyzed, beginning with an initial alignment using MAFFT and following with recombination analysis using Simplot and Bootscan. Only the window size and step size were altered for the genome analysis (1000 and 200, respectively), with the rest of the default parameters unchanged. Genome nucleotide positions are noted along the x-axis, and the percentages of permutated trees that supported grouping are marked along the y-axis. For reference, select genome and gene-specific landmarks are noted above each graph. Colors: pink, SAdV-E26 and green, HAdV-B16.
Bootscanning, 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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bootscaning tool  (Simplot Science)
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Simplot Science bootscaning tool
Nucleotide sequence recombination analysis of the whole genome and the hexon gene of HAdV-E4FSl. The genome of HAdV-E4FSl (AY599837) was analyzed for sequence recombination events with HAdV and SAdV genomes using the software Simplot, which is available on-line (http://sray.med.som.jhmi.edu/SCRoftware/simplot/). <t>Bootscan</t> analysis of the genome (A) and hexon (B) shows a lateral transfer of a portion of the hexon gene from HAdV-B 16. These are supported by the Simplot analysis of the genome (C) and hexon (D). Unlike the Simplot panels (C and D), only the SAdV-E26 genome, rather than the entire set of SAdV-E22 through -E26 sequences, is presented in the Bootscan panels (A and B), as similar genomes compete out the signal. For Bootscan, removing four of the five genomes and repeating the analysis with each individually, gives a clearer representation, reflecting the Simplot result for the highest similarity match. MAFFT software was used to align the sequences prior to recombination analysis (http://mafft.cbrc.jp/alignment/server/). Default parameter settings for the Simplot software were used for analyzing the hexon sequences: window size (200 nucleotides [nt]), step size (20 nt), replicates used (n=100), gap stripping (on), distance model (Kimura) and tree model (neighbor-joining). Similarly, whole genomes were analyzed, beginning with an initial alignment using MAFFT and following with recombination analysis using Simplot and Bootscan. Only the window size and step size were altered for the genome analysis (1000 and 200, respectively), with the rest of the default parameters unchanged. Genome nucleotide positions are noted along the x-axis, and the percentages of permutated trees that supported grouping are marked along the y-axis. For reference, select genome and gene-specific landmarks are noted above each graph. Colors: pink, SAdV-E26 and green, HAdV-B16.
Bootscaning Tool, 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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bootscanning on neighbor-joining (nj) trees  (Simplot Science)
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Simplot Science bootscanning on neighbor-joining (nj) trees
Nucleotide sequence recombination analysis of the whole genome and the hexon gene of HAdV-E4FSl. The genome of HAdV-E4FSl (AY599837) was analyzed for sequence recombination events with HAdV and SAdV genomes using the software Simplot, which is available on-line (http://sray.med.som.jhmi.edu/SCRoftware/simplot/). <t>Bootscan</t> analysis of the genome (A) and hexon (B) shows a lateral transfer of a portion of the hexon gene from HAdV-B 16. These are supported by the Simplot analysis of the genome (C) and hexon (D). Unlike the Simplot panels (C and D), only the SAdV-E26 genome, rather than the entire set of SAdV-E22 through -E26 sequences, is presented in the Bootscan panels (A and B), as similar genomes compete out the signal. For Bootscan, removing four of the five genomes and repeating the analysis with each individually, gives a clearer representation, reflecting the Simplot result for the highest similarity match. MAFFT software was used to align the sequences prior to recombination analysis (http://mafft.cbrc.jp/alignment/server/). Default parameter settings for the Simplot software were used for analyzing the hexon sequences: window size (200 nucleotides [nt]), step size (20 nt), replicates used (n=100), gap stripping (on), distance model (Kimura) and tree model (neighbor-joining). Similarly, whole genomes were analyzed, beginning with an initial alignment using MAFFT and following with recombination analysis using Simplot and Bootscan. Only the window size and step size were altered for the genome analysis (1000 and 200, respectively), with the rest of the default parameters unchanged. Genome nucleotide positions are noted along the x-axis, and the percentages of permutated trees that supported grouping are marked along the y-axis. For reference, select genome and gene-specific landmarks are noted above each graph. Colors: pink, SAdV-E26 and green, HAdV-B16.
Bootscanning On Neighbor Joining (Nj) Trees, 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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bootscan method  (Simplot Science)
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Simplot Science bootscan method
Nucleotide sequence recombination analysis of the whole genome and the hexon gene of HAdV-E4FSl. The genome of HAdV-E4FSl (AY599837) was analyzed for sequence recombination events with HAdV and SAdV genomes using the software Simplot, which is available on-line (http://sray.med.som.jhmi.edu/SCRoftware/simplot/). <t>Bootscan</t> analysis of the genome (A) and hexon (B) shows a lateral transfer of a portion of the hexon gene from HAdV-B 16. These are supported by the Simplot analysis of the genome (C) and hexon (D). Unlike the Simplot panels (C and D), only the SAdV-E26 genome, rather than the entire set of SAdV-E22 through -E26 sequences, is presented in the Bootscan panels (A and B), as similar genomes compete out the signal. For Bootscan, removing four of the five genomes and repeating the analysis with each individually, gives a clearer representation, reflecting the Simplot result for the highest similarity match. MAFFT software was used to align the sequences prior to recombination analysis (http://mafft.cbrc.jp/alignment/server/). Default parameter settings for the Simplot software were used for analyzing the hexon sequences: window size (200 nucleotides [nt]), step size (20 nt), replicates used (n=100), gap stripping (on), distance model (Kimura) and tree model (neighbor-joining). Similarly, whole genomes were analyzed, beginning with an initial alignment using MAFFT and following with recombination analysis using Simplot and Bootscan. Only the window size and step size were altered for the genome analysis (1000 and 200, respectively), with the rest of the default parameters unchanged. Genome nucleotide positions are noted along the x-axis, and the percentages of permutated trees that supported grouping are marked along the y-axis. For reference, select genome and gene-specific landmarks are noted above each graph. Colors: pink, SAdV-E26 and green, HAdV-B16.
Bootscan Method, 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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Image Search Results


Nucleotide sequence recombination analysis of the whole genome and the hexon gene of HAdV-E4FSl. The genome of HAdV-E4FSl (AY599837) was analyzed for sequence recombination events with HAdV and SAdV genomes using the software Simplot, which is available on-line (http://sray.med.som.jhmi.edu/SCRoftware/simplot/). Bootscan analysis of the genome (A) and hexon (B) shows a lateral transfer of a portion of the hexon gene from HAdV-B 16. These are supported by the Simplot analysis of the genome (C) and hexon (D). Unlike the Simplot panels (C and D), only the SAdV-E26 genome, rather than the entire set of SAdV-E22 through -E26 sequences, is presented in the Bootscan panels (A and B), as similar genomes compete out the signal. For Bootscan, removing four of the five genomes and repeating the analysis with each individually, gives a clearer representation, reflecting the Simplot result for the highest similarity match. MAFFT software was used to align the sequences prior to recombination analysis (http://mafft.cbrc.jp/alignment/server/). Default parameter settings for the Simplot software were used for analyzing the hexon sequences: window size (200 nucleotides [nt]), step size (20 nt), replicates used (n=100), gap stripping (on), distance model (Kimura) and tree model (neighbor-joining). Similarly, whole genomes were analyzed, beginning with an initial alignment using MAFFT and following with recombination analysis using Simplot and Bootscan. Only the window size and step size were altered for the genome analysis (1000 and 200, respectively), with the rest of the default parameters unchanged. Genome nucleotide positions are noted along the x-axis, and the percentages of permutated trees that supported grouping are marked along the y-axis. For reference, select genome and gene-specific landmarks are noted above each graph. Colors: pink, SAdV-E26 and green, HAdV-B16.

Journal: Virology

Article Title: Computational analysis of four human adenovirus type 4 genomes reveals molecular evolution through two interspecies recombination events

doi: 10.1016/j.virol.2013.05.014

Figure Lengend Snippet: Nucleotide sequence recombination analysis of the whole genome and the hexon gene of HAdV-E4FSl. The genome of HAdV-E4FSl (AY599837) was analyzed for sequence recombination events with HAdV and SAdV genomes using the software Simplot, which is available on-line (http://sray.med.som.jhmi.edu/SCRoftware/simplot/). Bootscan analysis of the genome (A) and hexon (B) shows a lateral transfer of a portion of the hexon gene from HAdV-B 16. These are supported by the Simplot analysis of the genome (C) and hexon (D). Unlike the Simplot panels (C and D), only the SAdV-E26 genome, rather than the entire set of SAdV-E22 through -E26 sequences, is presented in the Bootscan panels (A and B), as similar genomes compete out the signal. For Bootscan, removing four of the five genomes and repeating the analysis with each individually, gives a clearer representation, reflecting the Simplot result for the highest similarity match. MAFFT software was used to align the sequences prior to recombination analysis (http://mafft.cbrc.jp/alignment/server/). Default parameter settings for the Simplot software were used for analyzing the hexon sequences: window size (200 nucleotides [nt]), step size (20 nt), replicates used (n=100), gap stripping (on), distance model (Kimura) and tree model (neighbor-joining). Similarly, whole genomes were analyzed, beginning with an initial alignment using MAFFT and following with recombination analysis using Simplot and Bootscan. Only the window size and step size were altered for the genome analysis (1000 and 200, respectively), with the rest of the default parameters unchanged. Genome nucleotide positions are noted along the x-axis, and the percentages of permutated trees that supported grouping are marked along the y-axis. For reference, select genome and gene-specific landmarks are noted above each graph. Colors: pink, SAdV-E26 and green, HAdV-B16.

Article Snippet: For Bootscan, removing four of the five genomes and repeating the analysis with each individually, gives a clearer representation, reflecting the Simplot result for the highest similarity match.

Techniques: Sequencing, Software, Stripping Membranes