ChromaClade

ChromaClade visualizes site-specific amino acid residues on phylogenetic trees to reveal lineage-specific substitutions and residue frequency patterns.

Key Features:

• Taxon annotation: Annotates taxon names in a phylogenetic tree with amino acids from corresponding sequence alignments.
• Residue color-coding: Applies residue-specific color codes to annotated residues to highlight amino acid identities.
• Branch coloring: Colors branches according to residues found at descendant tips to indicate residue distributions along lineages.
• Site-specific frequency visualization: Enables visual inspection of site-specific amino acid frequencies within the context of a phylogeny.
• Lineage-specific substitution detection: Highlights lineage-specific residues and key substitutions along internal branches to assist distinction of founder effects and convergent evolution.
• Evolutionary pattern illustration: Illustrates conservative, adaptive, and convergent evolution patterns at individual sites.
• Large-dataset applicability: Demonstrated utility for visualizing site-wise residue distributions in large datasets.

Scientific Applications:

• Viral evolution studies: Applied to human immunodeficiency virus (HIV) and influenza A virus datasets to visualize site-wise residue distributions.
• Detection of convergent evolution: Used to identify cases of convergent evolution by mapping identical residues onto the phylogeny.
• Identification of lineage-specific adaptations: Used to reveal lineage-specific residues and potential adaptive substitutions along internal branches.
• Distinguishing founder effects: Aids comparison of founder effects versus convergent changes by considering residue patterns in the phylogenetic context.

Methodology:

Annotates taxon names with amino acids from sequence alignments, applies residue-specific color codes, and colors branches according to residues found at descendant tips to identify lineage-specific residues and substitutions on internal branches.