Archaeopteryx.js: Web-based Visualization and Exploration of Annotated Phylogenetic Trees

Archaeopteryx.js: Web-based Visualization and Exploration of Annotated Phylogenetic Trees

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As part of the Virus Pathogen Resource (ViPR) and the Influenza Research Database (IRD) bioinformatics resources we have developed Archaeopteryx.js for the web-based visualization and exploration of annotated phylogenetic trees. A unique advantage of Archaeopteryx.js is its user-driven metadata-based visualization abilities, which allow for visual pattern recognition in phylogenetic data. For example, data (such as virus clade and subtype, host species, temporal and geographic information) can be visualized as label and node colors, node shapes, and sizes. Archaeopteryx.js is written in JavaScript, and thus can run in any modern web-browser; it is the online counterpart to the Archaeopteryx desktop program.

While Archaeopteryx.js is used in virus-centric bioinformatics resources, it is a general-purpose tool and can be incorporated effortlessly (no programing experience required) into any website. Even the data-driven visualizations can be adapted to any use-case, if the data to be visualized is properly encoded in the input. Currently, we provide parsers for New Hampshire and phyloXML formatted trees. Due to its expressiveness, phyloXML is the preferred format, and a prerequisite for data-driven visualizations.

Archaeopteryx.js has been designed to be both powerful and user friendly by providing features such as: user selectable data display (e.g. branch lengths, support values, taxonomic and sequence information), intuitive zooming and panning, tools for organizing trees, authoritative search functions (including regular expressions), and download/export of trees in a variety of formats. We focused on making Archaeopteryx.js suitable for analyzing large and complex gene trees. For this purpose, Archaeopteryx.js provides means for the visualization of gene duplications, automated sub-tree collapsing (such as collapsing by node depth and shared features), and selection and display of sub-trees.

Development

We are committed to continuously support and improve Archaeopteryx.js, which is freely available under an open source license at https://github.com/cmzmasek/archaeopteryx-js.

This work is funded by the National Institute of Allergy and Infectious Diseases (NIH/DHHS) under contract no. HHSN272201400028C.