PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization

Kreft, Łukasz; Botzki, Alexander; Coppens, Frederik; Vandepoele, Klaas; Bel, Michiel Van

doi:10.1093/bioinformatics/btx324

Cited by 174 publications

(111 citation statements)

References 5 publications

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“…A Minimum Spanning Tree (MST) based on ST types was created using BioNumerics v7.5 (Applied Maths, Sint-Martens-Latem, Belgium). A single nucleotide polymorphism (SNP) tree for all isolates was constructed by CSI Phylogeny v1.4, available at the Center for Genomic Epidemiology 5 , and visualized with genotypic data using PhyD3 (Kreft et al, 2017).…”

Section: Analysis Of Mlst and Clone Complexesmentioning

confidence: 99%

Antimicrobial Resistance and Virulence Gene Profiles of Methicillin-Resistant and -Susceptible Staphylococcus aureus From Food Products in Denmark

Andersen

Stegger

et al. 2019

Front. Microbiol.

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Foods may potentially serve as vehicles for the transmission of antimicrobial-resistant variants of Staphylococcus aureus that are important in a human clinical context. Further, retail food products can be a cause of staphylococcal food poisoning. For these reasons and to account for source attribution and risk assessment, detailed information on the population structure, resistance, and virulence profiles of S. aureus originating from retail food products is necessary. In the current study, whole-genome sequences from 88 S. aureus isolates were subjected to bioinformatics analyses in relation to sequence types, antimicrobial resistance, and virulence profiles.The sequence types (ST) identified belonged to 13 clonal complexes (CC) with CC5 and CC398 being the most common. CC398 was identified as the dominant clone (n = 31). CC5 was identified as of avian origin, with the presence of ϕAVβ prophage genes (n = 13). In total, 39.8% of the isolates contained multiple resistance genes, and methicillinresistant Staphylococcus aureus (MRSA) isolates were found in CC8, CC9, and CC398. Genes conferring resistance to the antimicrobial classes of β-lactams, tetracycline, and erythromycin were detected in this study, all of which are commonly used in Danish livestock production. The tst gene encoding the toxic shock syndrome toxin was for the first time identified in ST398 isolates, probably as a result of a single acquisition of a SaPI-like element. The sushi-CC398 isolates carrying the scn gene likely originated from a human reservoir, while the other isolates originated from livestock. Taken together, our results show that both human and animal reservoirs contribute to contamination in food products and that retail foods may serve as a vehicle of S. aureus between livestock and humans.

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Section: Analysis Of Mlst and Clone Complexesmentioning

confidence: 99%

Antimicrobial Resistance and Virulence Gene Profiles of Methicillin-Resistant and -Susceptible Staphylococcus aureus From Food Products in Denmark

Andersen

Stegger

et al. 2019

Front. Microbiol.

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“…Branch support was inferred from 100 pseudo-bootstrap replicates each. The trees were rooted at the midpoint [21] and visualized with PhyD3 [22].…”

Section: Genome Featuresmentioning

confidence: 99%

Capnocytophaga felis sp. nov. isolated from the feline oral cavity

Suzuki

Umeda

Kimura

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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Four strains, KC07070T, KC07105, 11 025B-8C and 11 026B-8-C, were isolated from the oral cavity of cats in 2007 or 2011 in Japan. These strains were Gram-stain-negative rods, exhibited gliding motility, grew in air with 5 % CO2 and showed catalase and oxidase activity. The sequences of 16S rRNA genes of the four strains were 100 % identical. Additionally, the sequences of 16S rRNA genes of KC07070T had identity to those of the type strains of Capnocytophaga canimorsus (97.7 %), Capnocytophaga cynodegmi (97.8 %) and Capnocytophaga canis (97.4 %) and 91.2–93.8% identity to those of other species of the genus Capnocytophaga . The major cellular fatty acids of KC07070T were iso-C15 : 0 (56.2 %) and summed feature 11 (14.9 %). The G+C content of the DNA from KC07070T was 35.6 mol%, and the genome size was 2.88 Mbp. KC07070T had digital DNA–DNA hybridization (dDDH) values of 26.2–27.6% and average nucleotide identity (ANI) values of 75.4–83.3 % to the type strains of the closest relatives, C. canimorsus , C. cynodegmi and C. canis . These results of phylogenetic analysis of 16S rRNA gene sequence, cellular fatty acids compositions and dDDH and ANI values indicate that strain KC07070T represents a novel species, for which we propose the name Capnocytophaga felis sp. nov., with type strain KC07070T (=JCM 32681T=DSM 107251T).

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“…Common examples are cases where the tree is a dendrogram that visualizes the hierarchical relationship of the items in a table [7]. Similar approaches have been used for visualizing phylogenies and attributes about the species they contain [28,31] or transactions associated with a hierarchy [4]. Surprisingly few techniques also visualize attributes for inner nodes in a tree.…”

Section: Multivariate Graph and Tree Visualizationmentioning

confidence: 99%

Juniper: A Tree+Table Approach to Multivariate Graph Visualization

Nobre

Streit

Lex

2019

IEEE Trans. Visual. Comput. Graphics

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Analyzing large, multivariate graphs is an important problem in many domains, yet such graphs are challenging to visualize. In this paper, we introduce a novel, scalable, tree+table multivariate graph visualization technique, which makes many tasks related to multivariate graph analysis easier to achieve. The core principle we follow is to selectively query for nodes or subgraphs of interest and visualize these subgraphs as a spanning tree of the graph. The tree is laid out linearly, which enables us to juxtapose the nodes with a table visualization where diverse attributes can be shown. We also use this table as an adjacency matrix, so that the resulting technique is a hybrid node-link/adjacency matrix technique. We implement this concept in Juniper and complement it with a set of interaction techniques that enable analysts to dynamically grow, restructure, and aggregate the tree, as well as change the layout or show paths between nodes. We demonstrate the utility of our tool in usage scenarios for different multivariate networks: a bipartite network of scholars, papers, and citation metrics and a multitype network of story characters, places, books, etc.

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PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 174 publications

References 5 publications

Antimicrobial Resistance and Virulence Gene Profiles of Methicillin-Resistant and -Susceptible Staphylococcus aureus From Food Products in Denmark

Antimicrobial Resistance and Virulence Gene Profiles of Methicillin-Resistant and -Susceptible Staphylococcus aureus From Food Products in Denmark

Capnocytophaga felis sp. nov. isolated from the feline oral cavity

Juniper: A Tree+Table Approach to Multivariate Graph Visualization

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