ChromaClade: combined visualisation of phylogenetic and sequence data

Area of Science:

• Bioinformatics
• Computational Biology
• Evolutionary Biology

Background:

• Analyzing amino acid frequencies aids in understanding biological variability and adaptation.
• Phylogenetic context is crucial to differentiate common descent from selection pressure and identify evolutionary events like founder effects versus convergent evolution.
• Visualizing sequence and phylogenetic data together can yield evolutionary insights.

Purpose of the Study:

• To develop a tool that integrates phylogenetic and sequence data for evolutionary visualization.
• To create an intuitive graphical user interface for analyzing sequence-residue patterns within a phylogenetic framework.
• To facilitate the identification of lineage-specific adaptations and evolutionary events.

Main Methods:

• Development of ChromaClade, a tool with a graphical user interface.
• Integration of ChromaClade with popular phylogenetic tree viewers.
• Color-annotated phylogenies highlighting residues at each site and taxon.
• Application to human immunodeficiency virus (HIV) and influenza A virus datasets.

Main Results:

• ChromaClade generates color-annotated phylogenies that visualize site-specific residues across taxa.
• The tool effectively identifies lineage-specific residues and key substitutions on internal branches.
• Demonstrated utility in analyzing conserved, adaptive, and convergent evolution in viral datasets.
• Successful application to human immunodeficiency virus and influenza A virus data.

Conclusions:

• ChromaClade provides a powerful method for visualizing site-wise residue distributions and evolutionary patterns.
• The approach is particularly effective for large datasets and complex evolutionary analyses.
• ChromaClade aids in distinguishing between different modes of evolution, such as convergent evolution.
• The software is accessible for Windows, macOS, and Unix/Linux systems, with source code available.