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phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics.

Stephen D Shank1, Steven Weaver2, Sergei L Kosakovsky Pond2

  • 1Department of Biology and Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, 19122, USA. sshank@temple.edu.

BMC Bioinformatics
|July 27, 2018
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Summary
This summary is machine-generated.

phylotree.js is a new JavaScript library for interactive phylogenetic tree visualization. It extends d3.js, enabling complex, responsive applications in computational biology and beyond.

Keywords:
D3Data visualizationJavaScriptPhylogenetics

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Data Visualization

Background:

  • Existing JavaScript packages for phylogenetic tree visualization are often rigid frameworks, limiting extensibility for novel use cases.
  • Current tools typically generate standalone widgets, hindering integration as middleware within larger applications.

Purpose of the Study:

  • To introduce phylotree.js, a flexible JavaScript library for creating interactive phylogenetic tree visualizations.
  • To provide a tool that facilitates the development of complex, responsive computational biology applications incorporating phylogenetic data.

Main Methods:

  • phylotree.js is built upon the d3.js data visualization framework.
  • The library implements abstractions and provides a documented API to enhance interoperability and extensibility.
  • User interactions with phylogenetic trees can be captured and communicated to other application components.

Main Results:

  • phylotree.js enables the creation of dynamic and interactive phylogenetic tree visualizations.
  • The library supports the development of sophisticated applications, such as tools for tree annotation, comparative sequence analysis, and interactive tanglegrams.
  • Its design promotes seamless integration with other software components.

Conclusions:

  • phylotree.js serves as a valuable tool and application module for diverse computational biology software.
  • The library is open-source, available on GitHub under the MIT license, promoting accessibility and adoption.