The paper introducing our new tree visualisation tool Phylo.io was just published in MBE.

Yet another tool to display trees, you might say, and indeed, so it is. But for all the tools that have been developed over the years, there are very few that scale to large trees, make it easy to compare trees side-by-side, and simply run in a browser on any computer or mobile device.

To fill this gap, we created Phylo.io.

Story behind the paper

The project started as a student summer internship project, with the aim of producing a tree visualiser that facilitates comparison of trees built on the same set of leaves. After reading the project description, Oscar Robinson, a brilliant student from the Computer Science department at UCL, decided to work on this project during a three month internship. He saw a chance to apply his experience in the development of web tools and to develop his knowledge in the field of data visualisation, one of his major interests.

Once Oscar started with the development of Phylo.io, he realised that only a few tools existed for visual comparison of two trees and either seemed to rely on old technology or were cumbersome to use. Especially this incentive lead him to develop our tool into a fully fledged online resource that is easy to use, platform independent and based on the newest javascript libraries (e.g. D3). Within three months, he managed to produce a prototype of the tool. However, due to the short length of the internship, some details still needed a bit of attention.

Luckily for me, I started my PostDoc in the Dessimoz Lab around that time. Being a novice in a computational lab, Christophe proposed to me to take over the project and bring it to completing as a way to kickstart my postdoc. Altough my computational background at that time did not include any experience in JavaScript programming, I anyway accepted the challenge and was eager to start learning the material. Especially my initial steep learning progress was facilitaed by the help of two other brilliant PhD students, Alex Vesztrocy and Clément Train. Once I acquired some basic understanding, I was able to resolve bugs and add some key missing functionalities such as automatic tree rerooting or persistent storage and sharing functionality.

What is phylo.io and what can it do?

Phylo.io is a web tool that works in any modern browser. All computations are performed client-side and the only restriction on performace is the machine it is running on. Trees can be input in Newick and Extended Newick format. Phylo.io offers many features that other tree viewers have. Branches can be swapped, the rooting can be changed, the thickness, font and other parameters are adaptable. Many of these operations can be performed directly by clicking on a branch or a node in the tree. Importantly, it features an automatic subtree collapsing function: this facilitates the visualisation of large trees and hence the analysis of splits that are deep in the tree.

Next to basic tree visualisation/manipulation it features a compare mode. This mode allows to compare two trees computed using different tools or different models. Similarities and differences are highlighted using a colour scheme directly on the individual branches, making it clear where the differences in two topologies actually are. Additionally, since the output of different tools provides trees with very different rootings and leaf order, Phylo.io has a function to root one of the trees according to the other one and adapt the order of the leaves according to a fixed tree.

How do you use phylo.io?

To save you time, here is a one minute screencast highlighting some of the key features of Phylo.io:

You can find more info in the Phylo.io Manual.

Reference

Robinson, O., Dylus, D., & Dessimoz, C. (2016). Phylo.io: interactive viewing and comparison of large phylogenetic trees on the web

         <span style="font-style: italic;">Molecular Biology and Evolution</span> DOI: <a rev="review" href="http://dx.doi.org/10.1093/molbev/msw080">10.1093/molbev/msw080</a></span>