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

Journal: Viruses

Article Title: New Insights into Avian Infectious Bronchitis Virus in Colombia from Whole-Genome Analysis

doi: 10.3390/v14112562

Figure Lengend Snippet: ORF prediction and recombination analyses. ( a ) Genomic organization of V3, V10, V6, and V8. Red labels and yellow boxes highlight variation regions in detected ORFs. ( b ) and ( c ) Bootscan analysis (Simplot 3.5.1) of V6 and V8 whole genome sequences, respectively (windows size: 500 bp, step size: 100 bp). The dotted lines indicate a bootstrap value of 70%, and gray boxes indicate regions with recombination events.

Article Snippet: Recombination analysis was performed using Bootscan analyses as implemented in Simplot v3.5.1 [ ].

Techniques:

Journal: Frontiers in Microbiology

Article Title: Identification of a new circulating recombinant form of human immunodeficiency virus type 1, CRF124_cpx involving subtypes A, G, H, and CRF27_cpx in Angola

doi: 10.3389/fmicb.2022.992640

Figure Lengend Snippet: Investigation of human immunodeficiency virus (HIV) genome recombination in HIV-1 samples from Angola. Bootscan analysis was performed in SimPlot software using a 400 nt sliding window and 20 nt increments. (A) Complete genome (ANG.44 and ANG.78), (B) Partial genome (ANG.05, ANG.71, and ANG.113), and (C) ANG.37. The legend in the lower corner indicates the colors that represent the different clades of HIV-1.

Article Snippet: Recombination analyses were performed using a Bootscan implemented in SimPlot v3.5.1 software with the following parameters: 400 nucleotides (nt) window, 20 nt increments, and NJ method under Kimura’s two-parameter correction with 100 bootstrap replicates ( ).

Techniques: Virus, Software

Journal: Frontiers in Microbiology

Article Title: Identification of a new circulating recombinant form of human immunodeficiency virus type 1, CRF124_cpx involving subtypes A, G, H, and CRF27_cpx in Angola

doi: 10.3389/fmicb.2022.992640

Figure Lengend Snippet: Determination of the new circulating recombinant form (CRF) among HIV-1 samples circulating in Angola. (A) Bootscan analysis of the sequence ANG.44 was performed in SimPlot software using a 400 nt sliding window and 20 nt increments. (B) Genomic structure of CRF124_cpx colored according to the HIV-1 subtyping. The mosaic map was generated using the Recombinant HIV-1 Drawing Tool ( https://www.hiv.lanl.gov/content/sequence/DRAW_CRF/recom_mapper.html ). The maximum likelihood tree (ML) was performed to confirmation of the HIV-1 subtype of each fragment. ML tree implementing nucleotide substitution model General Time Reversible (GTR), indicating the phylogenetic relationships between pure HIV-1 subtypes and CRF124_cpx sequences. ALRT values were represented only if >0.90.

Article Snippet: Recombination analyses were performed using a Bootscan implemented in SimPlot v3.5.1 software with the following parameters: 400 nucleotides (nt) window, 20 nt increments, and NJ method under Kimura’s two-parameter correction with 100 bootstrap replicates ( ).

Techniques: Recombinant, Sequencing, Software, Generated