Journal: Viruses

Article Title: Clinical, Laboratory, and Molecular Epidemiology of an Outbreak of Aseptic Meningitis Due to a Triple-Recombinant Echovirus in Ashburton, New Zealand

doi: 10.3390/v14040658

Figure Lengend Snippet: Whole genome Simplot BootScan analysis with the query sequence of strain NZ/Ashburton/17WQ2027G/2017-08-20 (accession number MW586892) compared to Echovirus E6 (accession number KP289439), E11 (accession number KP294524), and E30 (accession number KY888274) reference sequences. ( A ) Similarity plot analysis, ( B ) Bootscanning analysis on the putative recombinant strain and its parental sequences. The enterovirus genomic organization is shown in the top.

Article Snippet: A Simplot BootScan v. 3.5.1 [ ] analysis was applied to a ClustalW alignment of the de novo assembled enterovirus genome MW586892 (strain NZ/Ashburton/17WQ2027G/2017-08-20) with echovirus E6 (isolate E6/P735/2013/China, accession number KP289439), echovirus E11 (strain 520k-YN-CHN-2010, accession number KP294524) and echovirus E30 (strain 14-397 collected 2013, accession number KY888274) sequences.

Techniques: Sequencing, Recombinant

Journal: Epidemics

Article Title: Evolutionary and molecular analysis of the emergent severe fever with thrombocytopenia syndrome virus

doi: 10.1016/j.epidem.2012.09.002

Figure Lengend Snippet: Putative mosaic structure of the RdRp gene of isolate 0723L-WDY. The partial gene sequence of RdRp (2194–3105 nt; HQ179724 ) of 0723L-WDY was analysed. (A) Similarity plot, (B) Bootscanning analysis (with GARD estimates of the breakpoint position shown in black) and (C) phylogenetic analysis of the regions on either side of the estimated breakpoint (position 432 nt). Bootstrapping analysis with 1000 pseudo-replicates was performed. Window and step sizes of 150 nt and 5 nt were used in the similarity plot and bootscanning analyses.

Article Snippet: Putative mosaic sequences were subsequently analysed using the similarity plot and bootscanning methods implemented in SIMPLOT v3.5 ( ).

Techniques: Sequencing

Journal: PLoS ONE

Article Title: Analysis of HIV-1 Protease Gene Reveals Frequent Multiple Infections Followed by Recombination among Drug Treated Individuals Living in São Paulo and Santos, Brazil

doi: 10.1371/journal.pone.0084066

Figure Lengend Snippet: We used the Neighbor-Joining method with K2P and 1000 bootstrap replicates. This analysis was performed using the software Simplot v3.5.1, with a window of 75 bp and 5 bp increments.

Article Snippet: Inter-subtype recombinants and breakpoints were investigated using Bootscan as implemented in the Simplot package v3.5.1 .

Techniques: Software