Abstract
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 analyzed). 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 large trees, high usability, multiplatform support via standard HTML5 implementation, and possibility to store and share visualizations. The tool can be freely accessed at http://phylo.io and can easily be embedded in other web servers. The code for the associated JavaScript library is available at https://github.com/DessimozLab/phylo-io under an MIT open source license.
Highlights
Phylogenetic analyses often require the inference and evaluation of multiple trees for the same group of taxa—either to gauge the uncertainty in the inference or to observe incongruence among different loci
The need for visualisation of large trees has driven the development of many different approaches, some of which are related to applications in biology
Multiple trees can be loaded simultaneously and it is possible to browse through each individual tree
Summary
Phylogenetic analyses often require the inference and evaluation of multiple trees for the same group of taxa—either to gauge the uncertainty in the inference (e.g. by sampling trees from the posterior distribution) or to observe incongruence among different loci (e.g. resulting from horizontal gene transfer). This tool allows to display basic newick trees and to manipulate a single tree. Similar to other tools, comparison of different trees is not supported. The best tools rely on colour coding and visual node annotation.
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