recombination analysis simplot software Search Results


simplot recombination analysis software  (Simplot Science)
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Simplot Science simplot recombination analysis software
IQ-TREE-generated maximum likelihood trees containing references and ( A ) all study sequences or ( B ) study sequences that were confirmed to be pure subtypes (including CRF01_AE) based on <t>recombination</t> analysis using SimPlot. Black lines indicate reference sequences used for subtype classification. Blue lines indicate sequences generated in this study. Surrounding labels indicate subtype/CRF locations on the tree. Red dots and neighboring values indicate important branch points on the tree and corresponding bootstrap values. The outgroup in both panels is SIV CPZ . Angled marks indicate that the branch length was truncated for visualization. Scale bars are included to show branch length diversity.
Simplot Recombination Analysis Software, supplied by Simplot Science, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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simplot recombination analysis software - by Bioz Stars, 2026-06
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IQ-TREE-generated maximum likelihood trees containing references and ( A ) all study sequences or ( B ) study sequences that were confirmed to be pure subtypes (including CRF01_AE) based on recombination analysis using SimPlot. Black lines indicate reference sequences used for subtype classification. Blue lines indicate sequences generated in this study. Surrounding labels indicate subtype/CRF locations on the tree. Red dots and neighboring values indicate important branch points on the tree and corresponding bootstrap values. The outgroup in both panels is SIV CPZ . Angled marks indicate that the branch length was truncated for visualization. Scale bars are included to show branch length diversity.

Journal: Viruses

Article Title: Next-Generation Sequencing Reveals Continued Circulation of Rare HIV-1 Subtypes in the Democratic Republic of the Congo and Refines the Estimate of the Emergence Dates of Three Subtypes

doi: 10.3390/v18020268

Figure Lengend Snippet: IQ-TREE-generated maximum likelihood trees containing references and ( A ) all study sequences or ( B ) study sequences that were confirmed to be pure subtypes (including CRF01_AE) based on recombination analysis using SimPlot. Black lines indicate reference sequences used for subtype classification. Blue lines indicate sequences generated in this study. Surrounding labels indicate subtype/CRF locations on the tree. Red dots and neighboring values indicate important branch points on the tree and corresponding bootstrap values. The outgroup in both panels is SIV CPZ . Angled marks indicate that the branch length was truncated for visualization. Scale bars are included to show branch length diversity.

Article Snippet: Specimen 146, which branched the most basal to subtype H references on this ML tree, was further analyzed by SimPlot recombination analysis software using DRC and reference subtype H sequences ( B,C).

Techniques: Generated

( A ) Subtype H branch of the ML tree from B. The red dot and number indicate the basal node of the branch with bootstrap value. ( B ) Similarity plot of the genome from specimen 146 (most basal H on the tree) comparing similarity between subtypes. ( C ) Bootscan of the genome from specimen 146 showing no evidence of recombination between subtypes. For SimPlot analysis in ( B , C ), all pure H subtypes from this study were included as references, and a window of 500 bp and step of 50 bp were used. For bootscanning, 1000 bootstrap replicates were used. To more clearly indicate sequences generated in this study, “_drc” was added to the specimen IDs in the figure. Subtype reference consensus sequences were used for SimPlot and Bootscan analyses.

Journal: Viruses

Article Title: Next-Generation Sequencing Reveals Continued Circulation of Rare HIV-1 Subtypes in the Democratic Republic of the Congo and Refines the Estimate of the Emergence Dates of Three Subtypes

doi: 10.3390/v18020268

Figure Lengend Snippet: ( A ) Subtype H branch of the ML tree from B. The red dot and number indicate the basal node of the branch with bootstrap value. ( B ) Similarity plot of the genome from specimen 146 (most basal H on the tree) comparing similarity between subtypes. ( C ) Bootscan of the genome from specimen 146 showing no evidence of recombination between subtypes. For SimPlot analysis in ( B , C ), all pure H subtypes from this study were included as references, and a window of 500 bp and step of 50 bp were used. For bootscanning, 1000 bootstrap replicates were used. To more clearly indicate sequences generated in this study, “_drc” was added to the specimen IDs in the figure. Subtype reference consensus sequences were used for SimPlot and Bootscan analyses.

Article Snippet: Specimen 146, which branched the most basal to subtype H references on this ML tree, was further analyzed by SimPlot recombination analysis software using DRC and reference subtype H sequences ( B,C).

Techniques: Generated