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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
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
TOOL
journal title
BIOINFORMATICS
Bioinformatics
volume
33
issue
18
pages
2946 - 2947
Web of Science type
Article
Web of Science id
000409541400024
ISSN
1367-4803
1460-2059
DOI
10.1093/bioinformatics/btx324
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
8533302
handle
http://hdl.handle.net/1854/LU-8533302
date created
2017-10-05 13:06:33
date last changed
2017-11-16 14:44:45
@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},
}

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.