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Interactive web-based visualization of phylogenetic trees using Phylogeny.IO

by Nikola Jovanovic and Alexander S Mikheyev

Traditional static publication formats make visualization, exploration and sharing of massive phylogenetic trees difficult. Web-based technologies, such as the Data Driven Document (D3) JavaScript library, exist to overcome such challenges by allowing interactive display of complex data sets. We here we an open-source web-based application that applies the power of D3 to the visualization of phylogenetic trees. Phylogeny.IO ( displays trees together with 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 shared as IFrame HTML objects easily embeddable in any web page.


The current server is hosted using DigitalOcean droplet, which is configured using LaravelForge.


Documentation is available at

Official URL



We would like to thank Marie Uemura for help in annotating the example tree with images from, and Evan Economo, as well as members of the Ecology and Evolution Unit for feedback on the project. We are grateful to Alopex Interaction Design LLC for creating the project logo. We are grateful for examples and open-source code by Rob Schmuecker, Ken-ichi Ueda, Jason Davies and Eric Shull. We would like to thank Abdullah Almsaeed for developing the AdmiLTE theme.

Funding for this work has been provided by the Okinawa Institute of Science and Technology Graduate University.

The Phylogeny.IO App is open-sourced software licensed under the MIT license