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Background <p>With the accumulation of phylogenomic data and the growing demand for bioinformatics analyses, it has become increasingly important and complex to construct evolutionary relationships for different research purposes. Therefore, the ability to support multiple scenarios has become an essential need for phylogenetic visualization.</p> Results <p>In this study, we present PhyloScape, a web-based application for interactive visualization of phylogenetic trees that can be used stand-alone or as a toolkit deployed on the users’ website. The platform supports customizable multiple visualization features and is equipped with a flexible metadata annotation system, providing researchers with publishable, interactive views of trees. PhyloScape extensions include views of amino acid identity, geometry, and protein structure, which are applicable to various areas such as microbial taxonomy, pathogen phylogeny, and plant conservation. Trees published on the website can be efficiently shared and integrated into the users’ own system via a unique address.</p> Conclusions <p>As a scalable platform, PhyloScape provides a variety of online plug-ins that users can easily combine for specific scenarios. PhyloScape is freely available at <a href="http://darwintree.cn/PhyloScape">http://darwintree.cn/PhyloScape</a>.</p>

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PhyloScape: interactive and scalable visualization platform for phylogenetic trees

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年7月10日

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  • Jiajia Wang,
  • Bo Zhang,
  • Linglu Zheng,
  • Yan Chen,
  • Chunyang Zhang,
  • Guojiao Lin,
  • Zhen Meng,
  • Xuezhi Wang,
  • Yuanchun Zhou

摘要

Background

With the accumulation of phylogenomic data and the growing demand for bioinformatics analyses, it has become increasingly important and complex to construct evolutionary relationships for different research purposes. Therefore, the ability to support multiple scenarios has become an essential need for phylogenetic visualization.

Results

In this study, we present PhyloScape, a web-based application for interactive visualization of phylogenetic trees that can be used stand-alone or as a toolkit deployed on the users’ website. The platform supports customizable multiple visualization features and is equipped with a flexible metadata annotation system, providing researchers with publishable, interactive views of trees. PhyloScape extensions include views of amino acid identity, geometry, and protein structure, which are applicable to various areas such as microbial taxonomy, pathogen phylogeny, and plant conservation. Trees published on the website can be efficiently shared and integrated into the users’ own system via a unique address.

Conclusions

As a scalable platform, PhyloScape provides a variety of online plug-ins that users can easily combine for specific scenarios. PhyloScape is freely available at http://darwintree.cn/PhyloScape.