Phylo.io

Phylo.io visualizes and compares phylogenetic trees to identify similarities, differences, and optimal rooting and leaf order for assessing evolutionary relationships among taxa, uncertainty in tree inference, and locus discordance.

Key Features:

• Side-by-Side Comparison: Compares two or more phylogenetic trees side-by-side to reveal concordant and discordant relationships among the same set of taxa.
• Highlighting Differences and Similarities: Automatically highlights matching and conflicting branches or clades between compared trees.
• Automatic Rooting and Leaf Order Matching: Identifies best matching rooting and optimizes leaf order between trees to improve structural alignment for comparison.
• Scalability to Large Trees: Handles large phylogenetic trees and datasets, enabling comparison beyond a few dozen taxa.
• Storage and Sharing Capabilities: Stores and shares phylogenetic tree visualizations for collaborative analysis.

Scientific Applications:

• Evolutionary biology: Comparing inferred phylogenies to study evolutionary relationships among taxa.
• Uncertainty analysis: Assessing uncertainty in tree inference by comparing alternative trees or replicates.
• Locus discordance analysis: Identifying and visualizing discordance among trees derived from different loci.

Methodology:

Performs side-by-side tree comparison with automatic highlighting of similarities and differences, automatic selection of matching rooting and leaf order, and supports storage and sharing of visualization outputs.