  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.
