Source-linked AI summary
Phylo.io: interactive viewing and comparison of large phylogenetic trees on the web
Oscar Robinson, David Dylus, Christophe Dessimoz
TL;DR
Researchers need to visualize and compare multiple large phylogenetic trees, but existing tools are poorly suited to side-by-side comparison beyond a few dozen taxa. Phylo.io provides web-based viewing and comparison with visual highlighting, automatic rooting and leaf-order matching, and scalability to large trees. It also supports saving and sharing visualisation states, facilitating collaborative work on large trees.
Problem
Existing phylogenetic-tree visualisation tools often do not support tree comparison and struggle with large trees or modern usability requirements.
Method
Phylo.io uses web-based side-by-side tree viewing and comparison with highlighted similarities and differences, automatic matching of rooting and leaf order, and single-tree viewing.
Results
Phylo.io supports large-tree visualisation while maintaining legibility and enables saving and sharing visualisation states for collaborative work.
Takeaways & Limitations
The tool provides a web-based way to compare large phylogenetic trees and share their visualisation states.
Takeaways & Limitations
The authors identify future work including support for other input formats and side-by-side comparison of trees with partially displayed content.
Abstract
from arXiv · showhide
Phylogenetic trees are pervasively used to depict evolutionary relationships. Increasingly, researchers need to visualize large trees and compare multiple large trees inferred for the same set of taxa (reflecting uncertainty in the tree inference or genuine discordance among the loci analysed). Existing tree visualization tools are however not well suited to these tasks. In particular, side-by-side comparison of trees can prove challenging beyond a few dozen taxa. Here, we introduce Phylo.io, a web application to visualize and compare phylogenetic trees side-by-side. Its distinctive features are: highlighting of similarities and differences between two trees, automatic identification of the best matching rooting and leaf order, scalability to very large trees, high usability, multiplatform support via standard HTML5 implementation, and possibility to store and share visualisations. The tool can be freely accessed at http://phylo.io. The code for the associated JavaScript library is available at https://github.com/DessimozLab/phylo-io under an MIT open source license.
INTRODUCTION
Researchers increasingly need to inspect and compare multiple large phylogenetic trees, but existing tools often lack comparison functions, scale poorly, or rely on outdated and difficult-to-use technology. Phylo.io addresses these gaps with web-based side-by-side comparison, visual highlighting, scalability, and sharing.
- Multiple trees for the same taxa help researchers assess inference uncertainty or incongruence among loci.
- Existing tools commonly lack functions for comparing different tree topologies and become cumbersome or illegible with very large trees.
- Aggregated visualisations, tanglegrams, and direct-comparison tools make specific differences difficult to identify or scale poorly as tree size increases.
- Current options also face usability and availability problems, including legacy browser requirements, platform restrictions, difficult installation, and discontinued maintenance.
- Phylo.io is a web-based tool for side-by-side tree viewing and comparison that uses colour schemes to show similarities and differences and highlight corresponding nodes and clades.
- Phylo.io supports large, legible trees, quantitative structural comparison, automatic matching of rooting and leaf order, and saved visualisation states shared through custom URLs.
NEW APPROACH
Phylo.io is a browser-based tree viewer that supports single-tree manipulation and side-by-side comparison of large trees. It combines automatic visual simplification, correspondence matching, interactive exploration, and shareable visualisations.
- The application is implemented with standard web technologies and released as permissive open source, while future work includes additional input formats and partially overlapping leaf sets.
- Phylo.io provides “view” and “compare” modes for displaying one tree or two trees side by side, with similarities and differences highlighted.
- Automatic node collapsing keeps large trees legible and accelerates rendering by representing deeper subtrees as composite triangular nodes.Collapsing is estimated from screen size; underlying data remain available while collapsed subtrees are not rendered.
- Trees with 500 taxa render in a few seconds on a laptop, while deferred subtree-comparison calculations help keep the interface responsive.
- Phylo.io supports search, basic tree operations, client-side computation, and sharing through unique URLs backed by the GitHub Gist API.
- The comparison workflow computes corresponding nodes, matching roots, and leaf orders, while automated branch swapping seeks the best corresponding visualisation.
- Selecting a node highlights and centers its counterpart in the other tree, expanding collapsed paths when necessary to reveal the matching structure.
- In a 737-protein example, Phylo.io showed that apparent differences between PhyML and RAxML trees were mostly caused by rooting and subtree ordering.
Funding
The work acknowledges support from UCL and the Swiss National Science Foundation and UK BBSRC.
- OR was supported by a Summer Research Bursary from the UCL Department of Computer Science.
- DD and CD acknowledge Swiss National Science Foundation grant 150654 and UK BBSRC grant BB/M015009/1.