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

Lukasz Kreft (UGent) , Alexander Botzki (UGent) , Frederik Coppens (UGent) , Klaas Vandepoele (UGent) and Michiel Van Bel (UGent)
(2017) BIOINFORMATICS. 33(18). p.2946-2947
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
Motivation: Comparative and evolutionary studies utilize phylogenetic trees to analyze and visualize biological data. Recently, several web-based tools for the display, manipulation and annotation of phylogenetic trees, such as iTOL and Evolview, have released updates to be compatible with the latest web technologies. While those web tools operate an open server access model with a multitude of registered users, a feature-rich open source solution using current web technologies is not available. Results: Here, we present an extension of the widely used PhyloXML standard with several new options to accommodate functional genomics or annotation datasets for advanced visualization. Furthermore, PhyD3 has been developed as a lightweight tool using the JavaScript library D3.js to achieve a state-of-the-art phylogenetic tree visualization in the web browser, with support for advanced annotations. The current implementation is open source, easily adaptable and easy to implement in third parties' web sites. Availability and implementation: More information about PhyD3 itself, installation procedures and implementation links are available at http://phyd3.bits.vib.be and at http://github.com/vibbits/phyd3/. Supplementary information: Supplementary data are available at Bioinformatics online.
Keywords
TOOL

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Citation

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Chicago
Kreft, Lukasz, Alexander Botzki, Frederik Coppens, Klaas Vandepoele, and Michiel Van Bel. 2017. “PhyD3 : a Phylogenetic Tree Viewer with Extended phyloXML Support for Functional Genomics Data Visualization.” Bioinformatics 33 (18): 2946–2947.
APA
Kreft, L., Botzki, A., Coppens, F., Vandepoele, K., & Van Bel, M. (2017). PhyD3 : a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization. BIOINFORMATICS, 33(18), 2946–2947.
Vancouver
1.
Kreft L, Botzki A, Coppens F, Vandepoele K, Van Bel M. PhyD3 : a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization. BIOINFORMATICS. 2017;33(18):2946–7.
MLA
Kreft, Lukasz, Alexander Botzki, Frederik Coppens, et al. “PhyD3 : a Phylogenetic Tree Viewer with Extended phyloXML Support for Functional Genomics Data Visualization.” BIOINFORMATICS 33.18 (2017): 2946–2947. Print.
@article{8533302,
  abstract     = {Motivation: Comparative and evolutionary studies utilize phylogenetic trees to analyze and visualize biological data. Recently, several web-based tools for the display, manipulation and annotation of phylogenetic trees, such as iTOL and Evolview, have released updates to be compatible with the latest web technologies. While those web tools operate an open server access model with a multitude of registered users, a feature-rich open source solution using current web technologies is not available. 
Results: Here, we present an extension of the widely used PhyloXML standard with several new options to accommodate functional genomics or annotation datasets for advanced visualization. Furthermore, PhyD3 has been developed as a lightweight tool using the JavaScript library D3.js to achieve a state-of-the-art phylogenetic tree visualization in the web browser, with support for advanced annotations. The current implementation is open source, easily adaptable and easy to implement in third parties' web sites. 
Availability and implementation: More information about PhyD3 itself, installation procedures and implementation links are available at http://phyd3.bits.vib.be and at http://github.com/vibbits/phyd3/.
Supplementary information: Supplementary data are available at Bioinformatics online.},
  author       = {Kreft, Lukasz and Botzki, Alexander and Coppens, Frederik and Vandepoele, Klaas and Van Bel, Michiel},
  issn         = {1367-4803},
  journal      = {BIOINFORMATICS},
  keyword      = {TOOL},
  language     = {eng},
  number       = {18},
  pages        = {2946--2947},
  title        = {PhyD3 : a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization},
  url          = {http://dx.doi.org/10.1093/bioinformatics/btx324},
  volume       = {33},
  year         = {2017},
}

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