Abstract
Traditional static publication formats make visualization, exploration, and sharing of massive phylogenetic trees difficult. A phylogenetic study often involves hundreds of taxa, and the resulting tree has to be split across multiple journal pages, or be shrunk onto one, which jeopardizes legibility. Furthermore, additional data layers, such as species-specific information or time calibrations are often displayed in separate figures, making the entire picture difficult for readers to grasp. Web-based technologies, such as the Data Driven Document (D3) JavaScript library, were created to overcome such challenges by allowing interactive displays of complex data sets. The new phylogeny.IO web server (https://phylogeny.io) overcomes this issue by allowing users to easily import, annotate, and share interactive phylogenetic trees. It allows a range of static (e.g. such as shapes and colors) and dynamic (e.g. pop-up text and images) annotations. Annotated trees can be saved on the server for subsequent modification or they may be shared as IFrame HTML objects, easily embeddable in any web page. The principal goal of phylogeny.IO is not to produce publication-ready figures, but rather to provide a simple and intuitive annotation interface that allows easy and rapid sharing of figures in blogs, lecture notes, press releases, etc.
Highlights
Traditional static publishing formats struggle to display complex data sets, including large phylogenetic trees. Such trees become split across multiple figures, sometimes spanning several pages, which makes them difficult to navigate, or else they are reduced in size, which makes them difficult to read
Phylogeny.IO allows users to implement a wide range of phylogenetic visualizations, and to share them with readers in any HTML document
The web server will be housed using state-of-the-art infrastructure at the Okinawa Institute of Science and Technology Graduate University, which will allow the site to scale with any increases in computational demand and popularity
Summary
Traditional static publishing formats struggle to display complex data sets, including large phylogenetic trees. Spreading layers of information across multiple figures renders it difficult to see how they interrelate, and can increase publication costs, which are often based on the number of color figures In response to these limitations, a wide range of electronic solutions have been developed to help visualize trees, including EvolView, iTol, Icy Tree, and PhyloWidget [1,2,3,4,5] (See [7] for a general review of visualization software). The phylotree.js library enables interactive trees to be included in web applications [7] These applications have rich feature sets, and produce beautifully rendered, sometimes publication-ready figures. They tend to focus on visualization of the tree within the application itself, either installed locally or via a web server interface
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