VIB Bioinformatics Core, VIB, 9052 Ghent, Belgium.
Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
Bioinformatics. 2017 Sep 15;33(18):2946-2947. doi: 10.1093/bioinformatics/btx324.
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.
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.
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/ .
klaas.vandepoele@ugent.vib.be or michiel.vanbel@ugent.vib.be.
Supplementary data are available at Bioinformatics online.
比较和进化研究利用系统发育树来分析和可视化生物数据。最近，一些用于显示、操作和注释系统发育树的基于网络的工具，如 iTOL 和 Evolview，已经发布了更新版本以与最新的网络技术兼容。虽然这些网络工具采用了开放的服务器访问模型，有大量注册用户，但没有使用当前网络技术的功能丰富的开源解决方案。
在这里，我们提出了广泛使用的 PhyloXML 标准的扩展，增加了几个新选项，以适应功能基因组学或注释数据集的高级可视化。此外，PhyD3 是使用 JavaScript 库 D3.js 开发的轻量级工具，用于在网络浏览器中实现最先进的系统发育树可视化，支持高级注释。当前的实现是开源的，易于适应和易于在第三方网站上实现。
有关 PhyD3 本身、安装过程和实现链接的更多信息，请访问 http://phyd3.bits.vib.be 和 http://github.com/vibbits/phyd3/ 。
klaas.vandepoele@ugent.vib.be 或 michiel.vanbel@ugent.vib.be。
补充数据可在 Bioinformatics 在线获得。
