Abstract
BackgroundMany software packages have been developed to address the need for generating phylogenetic trees intended for print. With an increased use of the web to disseminate scientific literature, there is a need for phylogenetic trees to be viewable across many types of devices and feature some of the interactive elements that are integral to the browsing experience. We propose a novel approach for publishing interactive phylogenetic trees.Methods/Principal FindingsWe present a javascript library, jsPhyloSVG, which facilitates constructing interactive phylogenetic trees from raw Newick or phyloXML formats directly within the browser in Scalable Vector Graphics (SVG) format. It is designed to work across all major browsers and renders an alternative format for those browsers that do not support SVG. The library provides tools for building rectangular and circular phylograms with integrated charting. Interactive features may be integrated and made to respond to events such as clicks on any element of the tree, including labels.Conclusions/SignificancejsPhyloSVG is an open-source solution for rendering dynamic phylogenetic trees. It is capable of generating complex and interactive phylogenetic trees across all major browsers without the need for plugins. It is novel in supporting the ability to interpret the tree inference formats directly, exposing the underlying markup to data-mining services. The library source code, extensive documentation and live examples are freely accessible at www.jsphylosvg.com.
Highlights
Constructing phylogenetic trees is a fundamental task in multiple fields of biology, including evolutionary, genetic, molecular and conservational biology
We introduce a novel javascript library for phylogenetic visualizations, jsPhyloSVG, which addresses many of the fundamental challenges involved with viewing phylogenetic trees online, including: generating scalable, navigatable trees that render in all major browsers without the need for plugins, integrating complex charting and boasting interactive features
The Vector Markup Language (VML) format displays an identical tree but is unable to support the interactive features that Scalable Vector Graphics (SVG) is capable of
Summary
Constructing phylogenetic trees is a fundamental task in multiple fields of biology, including evolutionary, genetic, molecular and conservational biology. Many software packages [1,2,3,4] have been created to address the need for constructing trees as static images for use in printed literature. Online access to scientific literature has recently opened up new possibilities yet presents additional challenges, . Phylogenetic trees need to be presented at varying resolutions in order to be optimized for both large monitors and small mobile devices. We introduce a novel javascript library for phylogenetic visualizations, jsPhyloSVG, which addresses many of the fundamental challenges involved with viewing phylogenetic trees online, including: generating scalable, navigatable trees that render in all major browsers without the need for plugins, integrating complex charting and boasting interactive features
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