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