PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods

Nascimento, Marta; Sousa, A. O.; Ramírez, Mario; Francisco, Alexandre P.; Carriço, João André; Vaz, Cátia

doi:10.1093/bioinformatics/btw582

Cited by 331 publications

(247 citation statements)

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“…NG-MAST, MLST, and NG-STAR sequence typing was performed by using gene sequences extracted in silico from whole-genome sequencing (WGS) data and submitted to the NG-MAST (http://www.ng-mast.net/), Neisseria MLST (http://pubmlst.org/neisseria/), and NG-STAR (https://ngstar.canada.ca) websites to determine the respective STs. The relatedness of allelic profiles was visualized by using PHYLOViZ 2.0 (41,42) to produce a full goeBURST minimum spanning tree. MLST and NG-STAR CCs were defined by a single-locus variation in allelic profiles from a founding ST, while an NG-MAST CC was determined by 5 or more single-nucleotide polymorphisms of concatenated and aligned porB and tbpB sequences.…”

Section: Methodsmentioning

confidence: 99%

Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance, a Novel Antimicrobial Resistance Multilocus Typing Scheme for Tracking Global Dissemination of N. gonorrhoeae Strains

et al. 2017

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A curated Web-based user-friendly sequence typing tool based on antimicrobial resistance determinants in Neisseria gonorrhoeae was developed and is publicly accessible (https://ngstar.canada.ca). The N. gonorrhoeae Sequence Typing for Antimicrobial Resistance (NG-STAR) molecular typing scheme uses the DNA sequences of 7 genes (penA, mtrR, porB, ponA, gyrA, parC, and 23S rRNA) associated with resistance to ␤-lactam antimicrobials, macrolides, or fluoroquinolones. NG-STAR uses the entire penA sequence, combining the historical nomenclature for penA types I to XXXVIII with novel nucleotide sequence designations; the full mtrR sequence and a portion of its promoter region; portions of ponA, porB, gyrA, and parC; and 23S rRNA sequences. NG-STAR grouped 768 isolates into 139 sequence types (STs) (n ϭ 660) consisting of 29 clonal complexes (CCs) having a maximum of a single-locus variation, and 76 NG-STAR STs (n ϭ 109) were identified as unrelated singletons. NG-STAR had a high Simpson's diversity index value of 96.5% (95% confidence interval [CI] ϭ 0.959 to 0.969). The most common STs were NG-STAR ST-90 (n ϭ 100; 13.0%), ST-42 and ST-91 (n ϭ 45; 5.9%), ST-64 (n ϭ 44; 5.72%), and ST-139 (n ϭ 42; 5.5%). Decreased susceptibility to azithromycin was associated with NG-STAR ST-58, ST-61, ST-64, ST-79, ST-91, and ST-139 (n ϭ 156; 92.3%); decreased susceptibility to cephalosporins was associated with NG-STAR ST-90, ST-91, and ST-97 (n ϭ 162; 94.2%); and ciprofloxacin resistance was associated with NG-STAR ST-26, 98.0%). All isolates of NG-STAR ST-42, ST-43, ST-63, ST-81, and ST-160 (n ϭ 106) were susceptible to all four antimicrobials. The standardization of nomenclature associated with antimicrobial resistance determinants through an internationally available database will facilitate the monitoring of the global dissemination of antimicrobial-resistant N. gonorrhoeae strains.

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Section: Methodsmentioning

confidence: 99%

Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance, a Novel Antimicrobial Resistance Multilocus Typing Scheme for Tracking Global Dissemination of N. gonorrhoeae Strains

et al. 2017

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“…MLVA-11 was also used to determine phylogeographic relationships between our isolates and 528 isolates from MLVAbank including not available group (2), Africa group (4), America group (75), West Mediterranean group (77), China group (97), and East Mediterranean group (273). Minimum-spaning trees were constructed using the goeBURST algorithm with PHYOVIZ 2.0 (Francisco et al, 2012; Nascimento et al, 2017). MLVA-16 cluster analysis was extended to 194 B. melitensis strains including the Ulanqab isolates reported here.…”

Section: Methodsmentioning

confidence: 99%

MLVA Genotyping Characteristics of Human Brucella melitensis Isolated from Ulanqab of Inner Mongolia, China

Liu

Wang

et al. 2017

Front. Microbiol.

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Brucellosis is a serious public health problem in Ulanqab, which is a region located in the middle of the Inner Mongolia Autonomous Region adjacent to Shanxi and Hebei provinces. The disease is prevalent in both the latter provinces and Ulanqab with the highest prevalence of brucellosis occurring in Inner Mongolia. The MLVA-16 scheme is a genotyping tool for assessing genetic diversity and relationships among isolates. Moreover, this genotyping tool can also be applied to epidemiological trace-back investigations. This study reports the occurrence of at least two B. melitensis biovars (1 and 3) in Ulanqab, encompassing 22 and 94 isolates, respectively. B. melitensis biovar 3 was the predominant biovar in the area examined. Panel 1 (MLVA-8) identified three genotypes (42, 63, and 114), with genotype 42 (n = 101) representing 87% of the tested strains. MLVA-11 identified eight genotypes (116, 111, 297, 291, and 342–345) from 116 of the analyzed isolates. All of these isolates were identified as belonging to the East Mediterranean group. Genotype 116 (n = 94) was the predominant genotype and represented 81% of the isolates. The isolates pertaining to this genotype were distributed throughout most of Ulanqab and neighboring regions. The MLVA-16 scheme showed the presence of 69 genotypes, with 46 genotypes being represented by single isolates. This analysis revealed that Ulanqab brucellosis cases had epidemiologically unrelated and sporadic characteristics. The remaining 23 genotypes were shared (between a total of 70 isolates) with each genotype being represented by two to eight isolates. These data indicate that these cases were epidemiologically related. MLVA genotyping confirmed the occurrence of a multipoint outbreak epidemic and intrafamilial brucellosis. Extensive genotype-sharing events were observed among isolates from different regions of Ulanqab and from other provinces of China. These findings suggest either a lack of control of animal movement between different regions or the circulation of contaminated animal products in the market. Our study is the first comprehensive genotyping and genetic analysis of B. melitensis in Ulanqab. We believe that this study will help to improve the effectiveness of brucellosis control programs.

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“…Phylograms may, however, be problematic for the presentation of large numbers of genotypes because Dendroscope (Huson and Scornavacca 2012)) from large datasets were also difficult to interpret. Still other graphical user interfaces were unable to even depict this large number of items, including PHYLOViZ 2.0 (Nascimento et al 2017), SplitsTree4 (Huson and Bryant 2006), EvolView (He et al 2016), Microreact (Argimon et al 2016), TreeDyn (Chevenet et al 2006),TreeView (Page 1996 and Phandango (Hadfield et al 2018).…”

Section: Introductionmentioning

confidence: 99%

“…An alternative to phylograms are minimum spanning trees, which have less demanding graphical requirements because they map clusters of related nodes in 2-D space (Francisco et al 2012;Nascimento et al 2017). A commercial software program (Bionumerics, Applied Maths, Belgium) introduced an improved visualization of a minimum spanning tree to microbiologists in the early 1990s, which reduced complexity by grouping isolates with identical STs within single nodes whose diameter reflected the numbers of isolates.…”

Section: Introductionmentioning

confidence: 99%

GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens

et al. 2018

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Current methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic profiles by a static "GrapeTree Layout" algorithm which supports interactive visualizations of large trees within a web browser window. GrapeTree also implements a novel minimum spanning tree algorithm (MSTree V2) to reconstruct genetic relationships despite high levels of missing data. GrapeTree is a stand-alone package for investigating phylogenetic trees plus associated metadata, and is also integrated into EnteroBase to facilitate cutting edge navigation of genomic relationships among bacterial pathogens.

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PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods

Abstract: cvaz@inesc-id.ptSupplementary information: Supplementary data are available at Bioinformatics online.

Cited by 331 publications

References 9 publications

Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance, a Novel Antimicrobial Resistance Multilocus Typing Scheme for Tracking Global Dissemination of N. gonorrhoeae Strains

Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance, a Novel Antimicrobial Resistance Multilocus Typing Scheme for Tracking Global Dissemination of N. gonorrhoeae Strains

MLVA Genotyping Characteristics of Human Brucella melitensis Isolated from Ulanqab of Inner Mongolia, China

GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens

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